Aptamer: Difference between revisions

Content deleted Content added

Inline

Revision as of 20:55, 3 July 2022

Aptamers (APT-uh-murz) are short sequences of artificial DNA or RNA that bind a specific target molecule. Like antibodies, which are used for similar purposes in biotechnology and medicine, they can show strong binding to their target, with little or no off-target binding^[1].

Most aptamers originate from SELEX (sounds like "selects"), a family of test-tube experiments for finding useful aptamers in a massive pool of different DNA sequences^[2]. This process is much like natural selection, and has been called "directed evolution" or "artificial selection." In SELEX, the researcher repeatedly selects for the best aptamers from a starting "library" made of about a quadrillion different randomly generated pieces of DNA or RNA. After SELEX, they might mutate or change the chemistry of the aptamers and do another selection^[3], or might use rational design processes to engineer improvements^[4]. Non-SELEX methods for discovering aptamers also exist^[5].

Researchers often want aptamers that show specific and sensitive binding to the chosen target; resist digestion by DNA- and RNA-destroying proteins; clear slowly from the body^[6]; change their shape dramatically when they bind their target^[7]; fit into a biosensor or in a test of a biological sample^[8]; have pre-defined levels or speeds of binding; and are small and cheap to make. To highlight how they are similar to and different from antibodies, aptamers are sometimes called “chemical antibodies.” Aptamers and antibodies can be used in many of the same tasks, but the nucleic acid-based structure of aptamers, which are mostly oligonucleotides, is very different from the amino acid-based structure of antibodies, which are proteins. This difference can make aptamers a better choice than antibodies for some purposes (see antibody replacement). Aptamers are used in biological lab research and clinical tests^[9], can measure large numbers of different proteins in a sample; identify molecular markers of disease^[10], or function as drugs^[11], drug delivery systems^[12] and controlled drug release systems^[13]. They also find use in other molecular engineering tasks^[14].

The first SELEX experiments were performed independently in 1990 by the Gold and Szostak labs^[15]. Commercial products and companies based on aptamers include the drug Macugen (pegaptanib)^[16] and the clinical diagnostic company SomaLogic^[17]. The International Society on Aptamers (INSOAP), a professional society for the aptamer research community, publishes a journal devoted to the topic, Aptamers. Apta-index is a current database cataloging and simplifying the ordering process for over 700 aptamers.

Etymology

The word "aptamer" is a neologism coined by Andrew Ellington and Jack Szostak in their first publication on the topic. They did not provide a precise definition, stating "We have termed these individual RNA sequences 'aptamers', from the Latin 'aptus', to fit."^[18]. Aptamers are occasionally referred to as "chemical antibodies" or "antibody mimics"^[19].

Researchers have coined many related labels and brand names, including "Spiegelmer," "SOMAmer," "smart aptamer," "optimer," "X-aptamer," "Raptamer," "aptabody," "affimer," and "peptide aptamer." No formal definition exists to exclude aptamers from non-aptamers, but the typical use is to describe a synthetically generated, nucleic acid-based ligand that is specific and sensitive for a particular target molecule.^[20]

History

The notion of selection in vitro or "directed evolution" had its roots in 1967, when Sol Spiegelman used a Qbeta replication system as a way to evolve a self-replicating molecule.^[21] In the ensuing decades, directed evolution was used to develop new functions in a range of bacterial proteins^[22]^[23]. A year before the publishing of the first SELEX and aptamers, Gerald Joyce used directed evolution to alter the cleavage activity of a ribozyme^[24].

In 1990, two labs independently developed SELEX and generated RNA aptamers: the Gold lab, using the term SELEX for their process of selecting RNA ligands against T4 DNA polymerase^[25]; and the Szostak lab, selecting RNA ligands against various organic dyes^[26]^[27]. Two years later, the Szostak lab and Gilead Sciences, acting independently of one another, used in vitro selection schemes to generate DNA aptamers for organic dyes^[28] and human thrombin^[29] (see anti-thrombin aptamers), respectively. In 2001, SELEX was automated by J. Colin Cox in the Ellington lab, reducing the duration of a selection experiment from a time-intensive process lasting several weeks to three days^[30]^[31]^[32].

In 2002, two groups led by Ronald Breaker and Evgeny Nudler published the first comprehensive proofs of a riboswitch, a nucleic acid-based genetic regulatory element, the existence of which had previously been suspected. Riboswitches possess similar molecular recognition properties to aptamers. In addition to the discovery of a new mode of genetic regulation, this added support to the 'RNA World hypothesis', a postulated stage in time in the origin of life on Earth^[33].

Properties

Structure

Most aptamers are based on a specific oligomer sequence of 20-100 bases and 3-20 kDa. Some have chemical modifications for functional enhancements or compatibility with larger engineered molecular systems. DNA, RNA, XNA, and peptide aptamer chemistries can each offer distinct profiles in terms of shelf stability, durability in serum or in vivo, specificity and sensitivity, cost, ease of generation, amplification, and characterization, and familiarity to users. Typically, nucleic acid aptamers exhibit low immunogenicity, are amplifiable via PCR, and have complex secondary structure and tertiary structure^[34]^[35]^[36]^[37]. DNA- and XNA-based aptamers exhibit superior shelf stability. XNA-based aptamers can introduce additional chemical diversity to increase binding affinity or greater durability in serum or in vivo. As 22 genetically-encoded and over 500 naturally-occurring amino acids exist, relative to the 4 nucleic acids in DNA or RNA, peptide aptamers, as well as antibodies, have much greater potential combinatorial diversity per unit length. It is, however, unclear to what extent this matters for practical purposes. Chemical modifications of nucleic acid bases or backbones increase the chemical diversity of standard nucleic acid bases. The unique structure of aptamer and target shapes non-covalent interactions between the two molecules and causes their selective binding, including via electrostatic interactions, hydrophobic interactions, pi stacking, and hydrogen bonding.

Split aptamers are composed of two or more DNA strands that are pieces of a larger parent aptamer that has been broken in two by a molecular nick^[38]. The ability of each component strand to bind targets will depend on the location of the nick, as well as the secondary structures of the daughter strands.^[39] The presence of a target molecule supports the DNA fragments joining together. This can be used as the basis for biosensors^[40]. Once assembled, the two separate DNA strands can be ligated into a single strand.

Non-modified aptamers are cleared rapidly from the bloodstream, with a half-life of seconds to hours. This is mainly due to nuclease degradation, which physically destroys the aptamers; as well as clearance by the kidneys, a result of the aptamer's low molecular weight. Several modifications, such as 2'-fluorine-substituted pyrimidines and polyethylene glycol (PEG) linkage, permit a serum half-life of days to weeks. PEGylation can add sufficient mass to prevent cleareance by the kidneys in vivo. Unmodified aptamers can treat transient conditions such as blood clotting, or organs such as the eye where the aptamer can be delivered without passing through the aptamer-destroying and -clearing serum. Rapid clearance from serum can also be useful in some applications, such as in vivo diagnostic imaging.

Targets

Aptamer targets can include small molecules and heavy metal ions, larger ligands such as proteins, and even whole cells.^[41]^[42]. These targets include lysozyme,^[43] thrombin,^[44] human immunodeficiency virus trans-acting responsive element (HIV TAR),^[45] hemin,^[46] interferon γ,^[47] vascular endothelial growth factor (VEGF),^[48] prostate specific antigen (PSA),^[49]^[50] dopamine,^[51] and the non-classical oncogene, heat shock factor 1 (HSF1).^[52]

Aptamers have been generated against cancer cells^[53], prions^[54], bacteria^[55], and viruses. Viral targets of aptamers include influenza A and B viruses,^[56] Respiratory syncytial virus (RSV),^[56] SARS coronavirus (SARS-CoV)^[56] and SARS-CoV-2^[57].

Aptamers may be particularly useful for environmental science proteomics^[58]. Antibodies, like other proteins, are more difficult to sequence than nucleic acids. They are also costly to maintain and produce, and at constant risk of contamination, as they are produced via cell culture or are harvested from animal serum. For this reason, researchers interested in little-studied proteins and species may find that companies will not produce, maintain, or validate the quality of antibodies against their target of interest.^[59]. By contrast, aptamers are simple to sequence and cost nothing to maintain, as their exact structure can be stored digitally and synthesized on demand. This may make them more economically feasible as research tools for underfunded biological research subjects. Aptamers exist for plant compounds, such as theophylline (found in tea)^[60] and abscisic acid (a plant immune hormone)^[61]. An aptamer against a-amanitin (the toxin that causes lethal amanita poisoning) has been developed, an example of an aptamer against a mushroom target^[62].

Peptide Aptamers

Structure

While most aptamers are based on nucleic acids, peptide aptamers ^[63] are artificial proteins selected or engineered to bind specific target molecules. These proteins consist of one or more peptide loops of variable sequence displayed by a protein scaffold. Derivatives known as tadpoles, in which peptide aptamer "heads" are covalently linked to unique sequence double-stranded DNA "tails", allow quantification of scarce target molecules in mixtures by PCR (using, for example, the quantitative real-time polymerase chain reaction) of their DNA tails.^[64] The peptides that form the aptamer variable regions are synthesized as part of the same polypeptide chain as the scaffold and are constrained at their N and C termini by linkage to it. This double structural constraint decreases the diversity of the conformations that the variable regions can adopt,^[65] and this reduction in conformational diversity lowers the entropic cost of molecular binding when interaction with the target causes the variable regions to adopt a single conformation.

Selection

The most common peptide aptamer selection system is the yeast two-hybrid system. Peptide aptamers can also be selected from combinatorial peptide libraries constructed by phage display and other surface display technologies such as mRNA display, ribosome display, bacterial display and yeast display. These experimental procedures are also known as biopanning. All the peptides panned from combinatorial peptide libraries have been stored in the MimoDB database.^[66]^[67]

Applications

Libraries of peptide aptamers have been used as "mutagens", in studies in which an investigator introduces a library that expresses different peptide aptamers into a cell population, selects for a desired phenotype, and identifies those aptamers that cause the phenotype. The investigator then uses those aptamers as baits, for example in yeast two-hybrid screens to identify the cellular proteins targeted by those aptamers. Such experiments identify particular proteins bound by the aptamers, and protein interactions that the aptamers disrupt, to cause the phenotype.^[68]^[69] In addition, peptide aptamers derivatized with appropriate functional moieties can cause specific postranslational modification of their target proteins, or change the subcellular localization of the targets.^[70]

Applications

This assay tests the ability of two different types of aptamers (V and I) to detect their respective protein targets (VEGF and IFN-y). The labels Apt1, Apt2, Apt3, and Apt4 are in decreasing order of binding strength (i.e. Apt1 is the strongest aptamer). The DD, AD, DA, and AA letters mean that they have different combinations of unnatural base pairs. This causes their difference in binding strengths. The "-" columns have no protein, and the "+" columns do have protein. Aptamer with protein (+) and without protein (-) is loaded into wells in a gel and moves down the column lanes. If target is present, they bind and travel more slowly, due to the charge on the aptamer and the mass of the protein. Otherwise, the unbound aptamer moves quickly to the end of the lane. The difference in position between the "+" and "-" bands is the "mobility shift." This allows the researcher to detect the presence or absence of the protein. The darker band in the leftmost V and I lanes show that stronger aptamer-target binding makes it easier to detect the target at a given amount of target protein in the sample. The bottom image includes denaturing urea in the gel that disrupts aptamer-target binding in the weaker I aptamers, showing that the aptamer-protein binding is indeed what caused the mobility shift.

Aptamer applications can be roughly grouped into sensing, therapeutic, and engineering categories. Sensing applications are important in environmental, biomedical, epidemiological, biosecurity, and basic research applications, where aptamers act as probes in assays, imaging methods, diagnostic assays, and biosensors^[41]^[71]^[72]^[73]^[74]^[75]. In therapeutic applications and precision medicine, aptamers can function as drugs^[76], targeted drug delivery vehicles^[77], as controlled release mechanisms, and as reagents for drug discovery via high-throughput screening for small molecules^[78] and proteins^[79]^[80]. They can function in molecular engineering applications as a way to modify proteins, such as enhancing DNA polymerase with hot start properties to make PCR more reliable^[81]^[82]^[83]^[84].

Antibody replacement

Aptamers can replace antibodies in many biotechnology applications^[85]^[86]. In laboratory research and clinical diagnostics, they can be used in aptamer-based versions of immunoassays including ELISA^[87], western blot^[88], IHC^[89], and flow cytometry^[90]. As therapeutics, they can function as agonists or antagonists of their ligand^[91]. While antibodies are a familiar technology with a well-developed market, aptamers are a relatively new technology to most researchers, and aptamers have been generated against only a fraction of important research targets^[92]. Unlike antibodies, unmodified aptamers are more susceptible to nuclease digestion in serum and renal clearance in vivo. Aptamers are much smaller in size and mass than antibodies, which could be a relevant factor in choosing which is best suited for a given application. When aptamers are available for a particular application, their advantages over antibodies include potentially lower immunogenicity, greater replicability and lower cost, a greater level of control due to the in vitro selection conditions, and capacity to be efficiently engineered for durability, specificity, and sensitivity^[93].

In addition, aptamers contribute to reduction of research animal use^[94]. While antibodies often rely on animals for initial discovery, as well as for production in the case of polyclonal antibodies, both the selection and production of aptamers is typically animal-free. However, note that phage display methods allow for selection of antibodies in vitro, followed by production from a monoclonal cell line, avoiding the use of animals entirely^[95].

Controlled release of therapeutics

The ability of aptamers to reversibly bind molecules such as proteins has generated increasing interest in using them to facilitate controlled release of therapeutic biomolecules, such as growth factors. This can be accomplished by tuning the binding strength to passively release the growth factors,^[96] along with active release via mechanisms such as hybridization of the aptamer with complementary oligonucleotides^[97] or unfolding of the aptamer due to cellular traction forces.^[98]

PCR

Aptamers have been used to create hot start functions in PCR enzymes to prevent non-specific amplification during the setup and initial phases of PCR reactions.^[99]

AptaBiD

AptaBiD (Aptamer-Facilitated Biomarker Discovery) is an aptamer-based method for biomarker discovery.^[100] AptaBiD involves discovering aptamers by using whole cells, rather than individual proteins, as the target. Aptamers bind to biomarkers on the surface of the cells in their native conformation. By selecting against binding ("negative selection") for one type of cell, such as an immature dendritic cell, and selecting for binding ("positive selection") the cell type of interest, such as a mature dendritic cell, researchers discover aptamers that bind biomarkers that distinguish one cell type from the other. Mass spectrometry can then be used to identify the biomarker, giving researchers both a novel aptamer and a novel biomarker for the cell type of interest in a single experiment. Such aptamers can be directly used for cell isolation, cell visualization, and tracking cells in vivo. They can also be used to control cell receptors to affect their behavior, and to deliver different agents, such as siRNA and drugs, into the specific cell type.

References

^ Crivianu-Gaita, Victor; Thompson, Michael (2016). "Aptamers, antibody scFv, and antibody Fab'fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements". Biosensors and Bioelectronics. 85: 32–45. doi:10.1016/j.bios.2016.04.091.
^ Gopinath, Subash (2007). "Methods developed for SELEX". Analytical and Bioanalytical Chemistry. 387: 171–182. doi:10.1007/s00216-006-0826-2. PMID 17072603. S2CID 23160358.
^ Gao, Shunxiang (2016). "Post-SELEX optimization of aptamers". Analytical and Bioanalytical Chemistry. 408 (17): 4567–4573. doi:10.1007/s00216-016-9556-2. PMID 27173394. S2CID 5411777.
^ Kalra, Priya (2018). "Simple methods and rational design for enhancing aptamer sensitivity and specificity". Frontiers in Molecular Biosciences. 5: 41. doi:10.3389/fmolb.2018.00041. PMC 5966647. PMID 29868605.
^ Berezovski, Maxim (2006). "Non-SELEX selection of aptamers". Journal of the American Chemical Society. 128 (5): 1410–1411. doi:10.1021/ja056943j.
^ Wang, R.E. (2011). "Improving the Stability of Aptamers by Chemical Modification". Current Medicinal Chemistry. 18 (27): 4126–4138. doi:10.2174/092986711797189565.
^ Feagin, Trevor; Maganzini, Nicolò; Soh, Hyongsok (2018). "Strategies for Creating Structure-Switching Aptamers". ACS Sensors. 3 (9): 1611–1615. doi:10.1021/acssensors.8b00516. PMID 30156834. S2CID 52120961.
^ Song, Shiping (2008). "Aptamer-based biosensors". TrAC Trends in Analytical Chemistry. 27 (2): 108–117. doi:10.1016/j.trac.2007.12.004.
^ Tombelli, Sara; Minunni, Maria; Mascini, Marco (2007). "Aptamers-based assays for diagnostics, environmental and food analysis". Biomolecular Engineering. 24 (2): 191–200. doi:10.1016/j.bioeng.2007.03.003. PMID 17434340.
^ Huang, Jie (2021). "Advances in aptamer-based biomarker discovery". Frontiers in Cell and Developmental Biology. 9: 659760. doi:10.3389/fcell.2021.659760. PMC 8007916. PMID 33796540.
^ Keefe, Anthony; Pai, Supriya; Ellington, Andrew (2010). "Aptamers as therapeutics". Nature Reviews Drug Discovery. 9 (7): 537–550. doi:10.1038/nrd3141. PMC 7097324. PMID 20592747.
^ Jiehua, Zhou; Rossi, John (2011). "Cell-specific aptamer-mediated targeted drug delivery". Oligonucleotides. 21 (1): 1–10. doi:10.1089/oli.2010.0264. PMC 3043981. PMID 21182455.
^ Farokhzad, Omid; Karp, Jeffrey; Langer, Robert (2006). "Nanoparticle-aptamer bioconjugates for cancer targeting". Expert Opinion on Drug Delivery. 3 (3): 311–324. doi:10.1517/17425247.3.3.311. S2CID 37058942.
^ Lin, Yun; Jayasena, Sumedha (1997). "Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer". Journal of Molecular Biology. 271: 100–111. doi:10.1006/jmbi.1997.1165. PMID 9300057.
^ Gold, Larry (2015). "SELEX: How it happened and where it will go". Journal of Molecular Evolution. 81 (5–6): 140–143. Bibcode:2015JMolE..81..140G. doi:10.1007/s00239-015-9705-9. PMC 4661202. PMID 26480964.
^ "FDA Approves Eyetech/Pfizer's Macugen". Review of Opthamology. Retrieved 30 June 2022.
^ Dutt, Sreetama. "SomaLogic and Illumina Combine Strengths to Propel Innovation in Proteomics". BioSpace. Retrieved 30 June 2022.
^ Ellington, Andrew; Szostak, Jack (1990). "In vitro selection of RNA molecules that bind specific ligands". Nature. 346 (6287): 818–822. Bibcode:1990Natur.346..818E. doi:10.1038/346818a0. PMID 1697402. S2CID 4273647.
^ Gang, Zhou (2016). "Aptamers: A promising chemical antibody for cancer therapy". Oncotarget. 7 (12): 13446–13463. doi:10.18632/oncotarget.7178. PMID 26863567. S2CID 16618423.
^ Joyce, Gerald (1994). "In vitro evolution of nucleic acids". Current Opinion in Structural Biology. 4 (3): 331–336. doi:10.1016/S0959-440X(94)90100-7. PMID 11539574.
^ Mills DR, Peterson RL, Spiegelman S (July 1967). "An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule". Proceedings of the National Academy of Sciences of the United States of America. 58 (1): 217–24. Bibcode:1967PNAS...58..217M. doi:10.1073/pnas.58.1.217. PMC 335620. PMID 5231602.
^ Francis, J.C.; Hansche, P.E. (1 January 1972). "DIRECTED EVOLUTION OF METABOLIC PATHWAYS IN MICROBIAL POPULATIONS. I. MODIFICATION OF THE ACID PHOSPHATASE pH OPTIMUM IN S. CEREVISIAE". Genetics. doi:10.1093/genetics/70.1.59. PMID 4552227.
^ Hall, Barry (1981). "Changes in the substrate specificities of an enzyme during directed evolution of new functions". Biochemistry. 20 (14): 4042–4049. doi:10.1021/bi00517a015. PMID 6793063.
^ Joyce, Gerald (1989). "Amplification, mutation and selection of catalytic RNA". Gene. 82: 83–87. doi:10.1016/0378-1119(89)90033-4.
^ Tuerk, Craig; Gold, Larry (1990). "Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase". Science. 249 (4968): 505–510. Bibcode:1990Sci...249..505T. doi:10.1126/science.2200121. PMID 2200121.
^ Ellington, Andrew; Szostak, Jack (1990). "In vitro selection of RNA molecules that bind specific ligands". Nature. 346 (6287): 818–822. Bibcode:1990Natur.346..818E. doi:10.1038/346818a0. S2CID 4273647.
^ Stoltenburg, Regina; Strehlitz, Beate (2007). "SELEX—a (r) evolutionary method to generate high-affinity nucleic acid ligands". Biomolecular Engineering. 24 (4): 381–403. doi:10.1016/j.bioeng.2007.06.001. PMID 17627883.
^ Ellington, Andrew; Szostak, Jack (1992). "Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures". Nature. 355 (6363): 850–852. Bibcode:1992Natur.355..850E. doi:10.1038/355850a0. PMID 1538766. S2CID 4332485.
^ Bock, Louis (1992). "Selection of single-stranded DNA molecules that bind and inhibit human thrombin". Nature. 355 (6360): 564–566. Bibcode:1992Natur.355..564B. doi:10.1038/355564a0. PMID 1741036. S2CID 4349607.
^ Cox JC, Ellington AD (October 2001). "Automated selection of anti-protein aptamers". Bioorganic & Medicinal Chemistry. 9 (10): 2525–31. doi:10.1016/s0968-0896(01)00028-1. PMID 11557339.
^ Cox JC, Rajendran M, Riedel T, Davidson EA, Sooter LJ, Bayer TS, et al. (June 2002). "Automated acquisition of aptamer sequences". Combinatorial Chemistry & High Throughput Screening. 5 (4): 289–99. doi:10.2174/1386207023330291. PMID 12052180.
^ Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, Ellington AD (October 2002). "Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer". Nucleic Acids Research. 30 (20): 108e–108. doi:10.1093/nar/gnf107. PMC 137152. PMID 12384610.
^ Breaker, Ronald (2012). "Riboswitches and the RNA world". Cold Spring Harbor Perspectives in Biology. 4 (2): a003566. doi:10.1101/cshperspect.a003566. PMC 3281570. PMID 21106649.
^ Svigelj R, Dossi N, Toniolo R, Miranda-Castro R, de-Los-Santos-Álvarez N, Lobo-Castañón MJ (September 2018). "Selection of Anti-gluten DNA Aptamers in a Deep Eutectic Solvent". Angewandte Chemie. 57 (39): 12850–54. Bibcode:2018AngCh.13013032S. doi:10.1002/ange.201804860. hdl:10651/49996. PMID 30070419. S2CID 240281828.
^ Neves MA, Reinstein O, Saad M, Johnson PE (December 2010). "Defining the secondary structural requirements of a cocaine-binding aptamer by a thermodynamic and mutation study". Biophysical Chemistry. 153 (1): 9–16. doi:10.1016/j.bpc.2010.09.009. PMID 21035241.
^ Baugh C, Grate D, Wilson C (August 2000). "2.8 A crystal structure of the malachite green aptamer". Journal of Molecular Biology. 301 (1): 117–28. doi:10.1006/jmbi.2000.3951. PMID 10926496.
^ Dieckmann T, Fujikawa E, Xhao X, Szostak J, Feigon J (1995). "Structural Investigations of RNA and DNA aptamers in Solution". Journal of Cellular Biochemistry. 59: 13–81. doi:10.1002/jcb.240590703. S2CID 221833821.
^ Chen, Ailiang; Yan, Mengmeng; Yang, Shuming (2016). "Split aptamers and their applications in sandwich aptasensors". TrAC Trends in Analytical Chemistry. 80: 581–593. doi:10.1016/j.trac.2016.04.006.
^ Kent AD, Spiropulos NG, Heemstra JM (October 2013). "General approach for engineering small-molecule-binding DNA split aptamers". Analytical Chemistry. 85 (20): 9916–23. doi:10.1021/ac402500n. PMID 24033257.
^ Debiais M, Lelievre A, Smietana M, Müller S (April 2020). "Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors". Nucleic Acids Research. 48 (7): 3400–22. doi:10.1093/nar/gkaa132. PMC 7144939. PMID 32112111.
^ ^a ^b Kaur H, Shorie M (2019). "Nanomaterial based aptasensors for clinical and environmental diagnostic applications". Nanoscale Advances. 1 (6): 2123–38. Bibcode:2019NanoA...1.2123K. doi:10.1039/C9NA00153K.
^ Mallikaratchy P (January 2017). "Evolution of Complex Target SELEX to Identify Aptamers against Mammalian Cell-Surface Antigens". Molecules. 22 (2): 215. doi:10.3390/molecules22020215. PMC 5572134. PMID 28146093.
^ Potty AS, Kourentzi K, Fang H, Jackson GW, Zhang X, Legge GB, Willson RC (February 2009). "Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor". Biopolymers. 91 (2): 145–56. doi:10.1002/bip.21097. PMID 19025993. S2CID 23670.
^ Long SB, Long MB, White RR, Sullenger BA (December 2008). "Crystal structure of an RNA aptamer bound to thrombin". RNA. 14 (12): 2504–12. doi:10.1261/rna.1239308. PMC 2590953. PMID 18971322.
^ Darfeuille F, Reigadas S, Hansen JB, Orum H, Di Primo C, Toulmé JJ (October 2006). "Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides". Biochemistry. 45 (39): 12076–82. doi:10.1021/bi0606344. PMID 17002307.
^ Liu M, Kagahara T, Abe H, Ito Y (2009). "Direct In Vitro Selection of Hemin-Binding DNA Aptamer with Peroxidase Activity". Bulletin of the Chemical Society of Japan. 82: 99–104. doi:10.1246/bcsj.82.99.
^ Min K, Cho M, Han SY, Shim YB, Ku J, Ban C (July 2008). "A simple and direct electrochemical detection of interferon-gamma using its RNA and DNA aptamers". Biosensors & Bioelectronics. 23 (12): 1819–24. doi:10.1016/j.bios.2008.02.021. PMID 18406597.
^ Ng EW, Shima DT, Calias P, Cunningham ET, Guyer DR, Adamis AP (February 2006). "Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease". Nature Reviews. Drug Discovery. 5 (2): 123–32. doi:10.1038/nrd1955. PMID 16518379. S2CID 8833436.
^ Savory N, Abe K, Sode K, Ikebukuro K (December 2010). "Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing". Biosensors & Bioelectronics. 26 (4): 1386–91. doi:10.1016/j.bios.2010.07.057. PMID 20692149.
^ Jeong S, Han SR, Lee YJ, Lee SW (March 2010). "Selection of RNA aptamers specific to active prostate-specific antigen". Biotechnology Letters. 32 (3): 379–85. doi:10.1007/s10529-009-0168-1. PMID 19943183. S2CID 22201181.
^ Walsh R, DeRosa MC (October 2009). "Retention of function in the DNA homolog of the RNA dopamine aptamer". Biochemical and Biophysical Research Communications. 388 (4): 732–35. doi:10.1016/j.bbrc.2009.08.084. PMID 19699181.
^ Salamanca HH, Antonyak MA, Cerione RA, Shi H, Lis JT (2014). "Inhibiting heat shock factor 1 in human cancer cells with a potent RNA aptamer". PLOS ONE. 9 (5): e96330. Bibcode:2014PLoSO...996330S. doi:10.1371/journal.pone.0096330. PMC 4011729. PMID 24800749.
^ Smith, Joshua (2007). "Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells". Analytical Chemistry. 3 (3): 311–324. doi:10.1517/17425247.3.3.311. PMID 16640493. S2CID 37058942. Retrieved 2 July 2022.
^ Proske, Daniela (2002). "Prion-protein-specific aptamer reduces PrPSc formation". ChemBioChem. 3 (8): 717–725. doi:10.1002/1439-7633(20020802)3:8<717::AID-CBIC717>3.0.CO;2-C. PMID 12203970. S2CID 36801266. Retrieved 2 July 2022.
^ Kaur H, Shorie M, Sharma M, Ganguli AK, Sabherwal P (December 2017). "Bridged Rebar Graphene functionalized aptasensor for pathogenic E. coli O78:K80:H11 detection". Biosensors & Bioelectronics. 98: 486–93. doi:10.1016/j.bios.2017.07.004. PMID 28728009.
^ ^a ^b ^c Asha K, Kumar P, Sanicas M, Meseko CA, Khanna M, Kumar B (December 2018). "Advancements in Nucleic Acid Based Therapeutics against Respiratory Viral Infections". Journal of Clinical Medicine. 8 (1): 6. doi:10.3390/jcm8010006. PMC 6351902. PMID 30577479.
^ Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G (April 2021). "A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism*". Angewandte Chemie. 60 (18): 10279–85. doi:10.1002/anie.202100316. PMC 8251191. PMID 33683787.
^ Dhar, Poshmaal; Samarasinghe, Rasika; Shigdar, Sarah (2020). "Antibodies, nanobodies, or aptamers—which is best for deciphering the proteomes of non-model species?". International Journal of Molecular Sciences. 21 (7): 2485. doi:10.3390/ijms21072485.
^ Bauer, Michelle (2019). "Anything you can do, I can do better: Can aptamers replace antibodies in clinical diagnostic applications?". Molecules. 24 (23): 4377. doi:10.3390/molecules24234377. PMC 6930532. PMID 31801185.
^ Feng, Silu (2018). "An aptamer nanopore-enabled microsensor for detection of theophylline". Biosensors and Bioelectronics. 105: 36–41. doi:10.1016/j.bios.2018.01.016. PMID 29351868. Retrieved 2 July 2022.
^ Song, Chao (2017). "Detection of plant hormone abscisic acid (ABA) using an optical aptamer-based sensor with a microfluidics capillary interface". 2017 IEEE 30th International Conference on Micro Electro Mechanical Systems (MEMS): 370–373. doi:10.1109/MEMSYS.2017.7863418. ISBN 978-1-5090-5078-9. S2CID 20781208.
^ Muszyńska, K.; Ostrowska, D.; Bartnicki, F.; Kowalska, E.; Bodaszewska-Lubaś, M.; Hermanowicz, P.; Strzałka, W. "Selection and analysis of a DNA aptamer binding α-amanitin from Amanita phalloides". Acta Biochimica Polonica. Retrieved 2 July 2022.
^ Colas P, Cohen B, Jessen T, Grishina I, McCoy J, Brent R (April 1996). "Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2". Nature. 380 (6574): 548–50. Bibcode:1996Natur.380..548C. doi:10.1038/380548a0. PMID 8606778. S2CID 4327303.
^ Nolan GP (January 2005). "Tadpoles by the tail". Nature Methods. 2 (1): 11–12. doi:10.1038/nmeth0105-11. PMID 15782163. S2CID 1423778.
^ Spolar RS, Record MT (February 1994). "Coupling of local folding to site-specific binding of proteins to DNA". Science. 263 (5148): 777–84. Bibcode:1994Sci...263..777S. doi:10.1126/science.8303294. PMID 8303294.
^ Huang J, Ru B, Zhu P, Nie F, Yang J, Wang X, et al. (January 2012). "MimoDB 2.0: a mimotope database and beyond". Nucleic Acids Research. 40 (Database issue): D271-7. doi:10.1093/nar/gkr922. PMC 3245166. PMID 22053087.
^ "MimoDB: a mimotope database and beyond". immunet.cn. Archived from the original on 2012-11-16. Retrieved 2016-02-03.
^ Geyer CR, Colman-Lerner A, Brent R (July 1999). ""Mutagenesis" by peptide aptamers identifies genetic network members and pathway connections". Proceedings of the National Academy of Sciences of the United States of America. 96 (15): 8567–72. Bibcode:1999PNAS...96.8567G. doi:10.1073/pnas.96.15.8567. PMC 17557. PMID 10411916.
^ Dibenedetto S, Cluet D, Stebe PN, Baumle V, Léault J, Terreux R, et al. (July 2013). "Calcineurin A versus NS5A-TP2/HD domain containing 2: a case study of site-directed low-frequency random mutagenesis for dissecting target specificity of peptide aptamers". Molecular & Cellular Proteomics. 12 (7): 1939–52. doi:10.1074/mcp.M112.024612. PMC 3708177. PMID 23579184.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Colas P, Cohen B, Ko Ferrigno P, Silver PA, Brent R (December 2000). "Targeted modification and transportation of cellular proteins". Proceedings of the National Academy of Sciences of the United States of America. 97 (25): 13720–25. Bibcode:2000PNAS...9713720C. doi:10.1073/pnas.97.25.13720. PMC 17642. PMID 11106396.
^ Penner, Gregory (July 2012). "Commercialization of an aptamer-based diagnostic test" (PDF). NeoVentures.
^ Wei H, Li B, Li J, Wang E, Dong S (September 2007). "Simple and sensitive aptamer-based colorimetric sensing of protein using unmodified gold nanoparticle probes". Chemical Communications (36): 3735–37. doi:10.1039/B707642H. PMID 17851611.
^ Cheng H, Qiu X, Zhao X, Meng W, Huo D, Wei H (March 2016). "Functional Nucleic Acid Probe for Parallel Monitoring K(+) and Protoporphyrin IX in Living Organisms". Analytical Chemistry. 88 (5): 2937–43. doi:10.1021/acs.analchem.5b04936. PMID 26866998.
^ Xiang Y, Lu Y (July 2011). "Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets". Nature Chemistry. 3 (9): 697–703. Bibcode:2011NatCh...3..697X. doi:10.1038/nchem.1092. PMC 3299819. PMID 21860458.
^ Agnivo Gosai, Brendan Shin Hau Yeah, Marit Nilsen-Hamilton, Pranav Shrotriya, "Label free thrombin detection in presence of high concentration of albumin using an aptamer-functionalized nanoporous membrane", Biosensors and Bioelectronics, Volume 126, 2019, pp. 88–95, ISSN 0956-5663, doi:10.1016/j.bios.2018.10.010.
^ Amero, Paola; Khatua, Soumen; Rodriguez-Aguayo, Cristian; Lopez-Berestein, Gabriel (October 2020). "Aptamers: Novel Therapeutics and Potential Role in Neuro-Oncology". Cancers. 12 (10): 2889. doi:10.3390/cancers12102889. PMC 7600320. PMID 33050158.
^ Fattal, Elias; Hillaireau, Hervé; Ismail, Said I. (September 2018). "Aptamers in Therapeutics and Drug Delivery". Advanced Drug Delivery Reviews. 134: 1–2. doi:10.1016/j.addr.2018.11.001. ISSN 1872-8294. PMID 30442313. S2CID 53562925.
^ Hafner M, Vianini E, Albertoni B, Marchetti L, Grüne I, Gloeckner C, Famulok M (2008). "Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization". Nature Protocols. 3 (4): 579–587. doi:10.1038/nprot.2008.15. PMID 18388939. S2CID 4997899.
^ Huang, Zike; Qiu, Liping; Zhang, Tao; Tan, Weihong (2021-02-03). "Integrating DNA Nanotechnology with Aptamers for Biological and Biomedical Applications". Matter. 4 (2): 461–489. doi:10.1016/j.matt.2020.11.002. ISSN 2590-2385. S2CID 234061584.
^ Reynaud, Lucile; Bouchet-Spinelli, Aurélie; Raillon, Camille; Buhot, Arnaud (January 2020). "Sensing with Nanopores and Aptamers: A Way Forward". Sensors. 20 (16): 4495. Bibcode:2020Senso..20.4495R. doi:10.3390/s20164495. PMC 7472324. PMID 32796729.
^ Keijzer, Jordi F.; Albada, Bauke (2022). "DNA-assisted site-selective protein modification". Biopolymers. 113 (3): e23483. doi:10.1002/bip.23483. ISSN 1097-0282. PMID 34878181. S2CID 244954278.
^ Smith, Drew; Collins, Brian D.; Heil, James; Koch, Tad H. (January 2003). "Sensitivity and Specificity of Photoaptamer Probes". Molecular & Cellular Proteomics. 2 (1): 11–18. doi:10.1074/mcp.m200059-mcp200. ISSN 1535-9476. PMID 12601078. S2CID 13406870.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Vinkenborg, Jan L.; Mayer, Günter; Famulok, Michael (2012-08-02). "Aptamer-Based Affinity Labeling of Proteins". Angewandte Chemie International Edition. 51 (36): 9176–9180. doi:10.1002/anie.201204174. ISSN 1433-7851. PMID 22865679.
^ Keijzer, Jordi F.; Firet, Judith; Albada, Bauke (2021). "Site-selective and inducible acylation of thrombin using aptamer-catalyst conjugates". Chemical Communications. 57 (96): 12960–12963. doi:10.1039/d1cc05446e. ISSN 1359-7345. PMID 34792071. S2CID 243998479.
^ Chen, Ailiang; Yang, Shuming (2015). "Replacing antibodies with aptamers in lateral flow immunoassay". Biosensors and Bioelectronics. 71: 230–242. doi:10.1016/j.bios.2015.04.041. PMID 25912679.
^ Bauer, Michelle (2019). "Anything you can do, I can do better: Can aptamers replace antibodies in clinical diagnostic applications?". Molecules. 24 (23): 4377. doi:10.3390/molecules24234377. PMC 6930532. PMID 31801185.
^ Toh, Saw Yi (2015). "Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay". Biosensors and Bioelectronics. 64: 392–403. doi:10.1016/j.bios.2014.09.026. PMID 25278480.
^ Bruno, J.G.; Sivils, J.C. (2016). "Aptamer "Western" blotting for E. coli outer membrane proteins and key virulence factors in pathogenic E. coli serotypes". Aptamers and Synthetic Antibodies.
^ Bauer, Michelle (2016). "The application of aptamers for immunohistochemistry". Nucleic Acid Therapeutics. 26 (3): 120–126. doi:10.1089/nat.2015.0569. PMID 26862683.
^ Meyer, Michael; Scheper, Thomas; Walter, Johanna-Gabriela (2013). "Aptamers: versatile probes for flow cytometry". Applied Microbiology and Biotechnology. 97 (16): 7097–7109. doi:10.1007/s00253-013-5070-z. PMID 23838792. S2CID 13996688.
^ Zhou, Jiehua; Rossi, John (2017). "Aptamers as targeted therapeutics: current potential and challenges". Nature Reviews Drug Discovery. 16 (3): 181–202. doi:10.1038/nrd.2016.199. PMC 5700751. PMID 27807347.
^ Bruno, John (2015). "Predicting the Uncertain Future of Aptamer-Based Diagnostics and Therapeutics". Molecules. 20 (4): 6866–6887. doi:10.3390/molecules20046866. PMC 6272696. PMID 25913927.
^ Wang, Tao (2019). "Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development". Biotechnology Advances. 37 (1): 28–50. doi:10.1016/j.biotechadv.2018.11.001. PMID 30408510. S2CID 53242220.
^ Melbourne, Jodie (2016). "A Multi-faceted Approach to Achieving the Global Acceptance of Animal-free Research Methods". Alternatives to Laboratory Animals. 44 (5): 495–498. doi:10.1177/026119291604400511. PMID 27805832. S2CID 1002312.
^ Alfaleh, Mohamed A. (2020). "Phage display derived monoclonal antibodies: from bench to bedside". Frontiers in Immunology. 11: 1986. doi:10.3389/fimmu.2020.01986. PMC 7485114. PMID 32983137.
^ Soontornworajit B, Zhou J, Shaw MT, Fan TH, Wang Y (March 2010). "Hydrogel functionalization with DNA aptamers for sustained PDGF-BB release". Chemical Communications. 46 (11): 1857–59. doi:10.1039/B924909E. PMID 20198232.
^ Battig MR, Soontornworajit B, Wang Y (August 2012). "Programmable release of multiple protein drugs from aptamer-functionalized hydrogels via nucleic acid hybridization". Journal of the American Chemical Society. 134 (30): 12410–13. doi:10.1021/ja305238a. PMID 22816442.
^ Stejskalová A, Oliva N, England FJ, Almquist BD (February 2019). "Biologically Inspired, Cell-Selective Release of Aptamer-Trapped Growth Factors by Traction Forces". Advanced Materials. 31 (7): e1806380. doi:10.1002/adma.201806380. PMC 6375388. PMID 30614086.
^ Sahara Hot Start PCR Master Mix
^ Berezovski MV, Lechmann M, Musheev MU, Mak TW, Krylov SN (July 2008). "Aptamer-facilitated biomarker discovery (AptaBiD)". Journal of the American Chemical Society. 130 (28): 9137–43. doi:10.1021/ja801951p. PMID 18558676.

@@ Line 4: / Line 4: @@
 [[File:Breast cancer spheroids with aptamers.png|thumb|450x330 px|[[Breast cancer]] cells incubated with aptamers that bind selectively to biomarkers on the cancer cells, but not to healthy cells. Aptamers are linked to [[fluorescein]], a molecule that glows red under [[UV]] light. This type of test allows a doctor or researcher to identify cancer cells in a [[biopsy|tissue sample from a patient]].]]
-'''Aptamers''' (APT-uh-murz) are [[oligomers|short sequences]] of artificial [[DNA]] or [[RNA]] that [[ligand|bind a specific target molecule]]. Like [[antibodies]], which are used for similar purposes in [[biotechnology]] and [[medicine]], they can show strong binding to their target, with little or no [[off-target]] binding<ref>{{cite journal |last1=Crivianu-Gaita |first1=Victor |last2=Thompson |first2=Michael |title=Aptamers, antibody scFv, and antibody Fab'fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements |journal=Biosensors and bioelectronics |date=2016 |doi=10.1016/j.bios.2016.04.091}}</ref>.
+'''Aptamers''' (APT-uh-murz) are [[oligomers|short sequences]] of artificial [[DNA]] or [[RNA]] that [[ligand|bind a specific target molecule]]. Like [[antibodies]], which are used for similar purposes in [[biotechnology]] and [[medicine]], they can show strong binding to their target, with little or no [[off-target]] binding<ref>{{cite journal |last1=Crivianu-Gaita |first1=Victor |last2=Thompson |first2=Michael |title=Aptamers, antibody scFv, and antibody Fab'fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements |journal=Biosensors and Bioelectronics |date=2016 |volume=85 |pages=32–45 |doi=10.1016/j.bios.2016.04.091}}</ref>.
-Most aptamers originate from [[Systematic evolution of ligands by exponential enrichment|SELEX]] (sounds like "selects"), a family of [[in vitro|test-tube experiments]] for finding useful aptamers in a massive pool of different DNA sequences<ref>{{cite journal |last1=Gopinath |first1=Subash |title=Methods developed for SELEX |journal=Analytical and Bioanalytical Chemistry |date=2007 |doi=10.1007/s00216-006-0826-2}}</ref>. This process is much like [[natural selection]], and has been called "[[directed evolution]]" or "artificial selection." In SELEX, the researcher repeatedly selects for the best aptamers from a starting "library" made of about a [[quadrillion]] different [[oligonucleotide synthesis|randomly generated pieces of DNA or RNA]]. After SELEX, they might [[mutate]] or [[bioconjugation|change the chemistry]] of the aptamers and do another selection<ref>{{cite journal |last1=Gao |first1=Shunxiang |title=Post-SELEX optimization of aptamers |journal=Analytical and bioanalytical chemistry |date=2016 |doi=10.1007/s00216-016-9556-2}}</ref>, or might use [[rational design]] processes to engineer improvements<ref>{{cite journal |last1=Kalra |first1=Priya |title=Simple methods and rational design for enhancing aptamer sensitivity and specificity |journal=Frontiers in molecular biosciences |date=2018 |doi=10.3389/fmolb.2018.00041}}</ref>. Non-SELEX methods for discovering aptamers also exist<ref>{{cite journal |last1=Berezovski |first1=Maxim |title=Non-SELEX selection of aptamers |journal=Journal of the American Chemical Society |date=2006 |doi=10.1021/ja056943j}}</ref>.
+Most aptamers originate from [[Systematic evolution of ligands by exponential enrichment|SELEX]] (sounds like "selects"), a family of [[in vitro|test-tube experiments]] for finding useful aptamers in a massive pool of different DNA sequences<ref>{{cite journal |last1=Gopinath |first1=Subash |title=Methods developed for SELEX |journal=Analytical and Bioanalytical Chemistry |date=2007 |volume=387 |pages=171–182 |doi=10.1007/s00216-006-0826-2|pmid=17072603 |s2cid=23160358 }}</ref>. This process is much like [[natural selection]], and has been called "[[directed evolution]]" or "artificial selection." In SELEX, the researcher repeatedly selects for the best aptamers from a starting "library" made of about a [[quadrillion]] different [[oligonucleotide synthesis|randomly generated pieces of DNA or RNA]]. After SELEX, they might [[mutate]] or [[bioconjugation|change the chemistry]] of the aptamers and do another selection<ref>{{cite journal |last1=Gao |first1=Shunxiang |title=Post-SELEX optimization of aptamers |journal=Analytical and Bioanalytical Chemistry |date=2016 |volume=408 |issue=17 |pages=4567–4573 |doi=10.1007/s00216-016-9556-2|pmid=27173394 |s2cid=5411777 }}</ref>, or might use [[rational design]] processes to engineer improvements<ref>{{cite journal |last1=Kalra |first1=Priya |title=Simple methods and rational design for enhancing aptamer sensitivity and specificity |journal=Frontiers in Molecular Biosciences |date=2018 |volume=5 |page=41 |doi=10.3389/fmolb.2018.00041|pmid=29868605 |pmc=5966647 |doi-access=free }}</ref>. Non-SELEX methods for discovering aptamers also exist<ref>{{cite journal |last1=Berezovski |first1=Maxim |title=Non-SELEX selection of aptamers |journal=Journal of the American Chemical Society |date=2006 |volume=128 |issue=5 |pages=1410–1411 |doi=10.1021/ja056943j}}</ref>.
-Researchers often want aptamers that show [[sensitivity and specificity|specific and sensitive]] binding to the chosen target; resist [[hydrolysis|digestion]] by [[nucleases|DNA- and RNA-destroying proteins]]; [[clearance (pharmacology)|clear slowly from the body]]<ref>{{cite journal |last1=Wang |first1=R.E. |title=Improving the Stability of Aptamers by Chemical Modification |journal=Current Medicinal Chemistry |date=2011 |doi=10.2174/092986711797189565}}</ref>; [[conformational change|change their shape dramatically when they bind their target]]<ref>{{cite journal |last1=Feagin |first1=Trevor |last2=Maganzini |first2=Nicolò |last3=Soh |first3=Hyongsok |title=Strategies for Creating Structure-Switching Aptamers |journal=ACS sensors |doi=10.1021/acssensors.8b00516}}</ref>; fit into a [[biosensor]] or in a [[assay|test of a biological sample]]<ref>{{cite journal |last1=Song |first1=Shiping |title=Aptamer-based biosensors |journal=TrAC Trends in Analytical Chemistry |date=2008 |url=https://www.sciencedirect.com/science/article/pii/S0165993607002658}}</ref>; have pre-defined [[equilibrium constant|levels]] or [[rate constant|speeds]] of binding; and are small and cheap to make. To highlight how they are similar to and different from antibodies, aptamers are sometimes called “[[antibody mimetic|chemical antibodies]].” Aptamers and antibodies can be used in many of the same tasks, but the [[nucleic acid]]-based structure of aptamers, which are mostly [[oligonucleotides]], is very different from the [[amino acid]]-based structure of antibodies, which are [[proteins]]. This difference can make aptamers a better choice than antibodies for some purposes (see [[Aptamer#Antibody_replacement|antibody replacement]]). Aptamers are used in biological lab research and clinical tests<ref>{{cite journal |last1=Tombelli |first1=Sara |last2=Minunni |first2=Maria |last3=Mascini |first3=Marco |title=Aptamers-based assays for diagnostics, environmental and food analysis |journal=Biomolecular engineering |date=2007 |doi=10.1016/j.bioeng.2007.03.003}}</ref>, can [[proteomics|measure large numbers of different proteins in a sample]];  [[biomarker discovery|identify molecular markers of disease]]<ref>{{cite journal |last1=Huang |first1=Jie |title=Advances in aptamer-based biomarker discovery |journal=Frontiers in Cell and Developmental Biology |date=2021 |doi=10.3389/fcell.2021.659760}}</ref>, or function as [[RNA therapeutics|drugs]]<ref>{{cite journal |last1=Keefe |first1=Anthony |last2=Pai |first2=Supriya |last3=Ellington |first3=Andrew |title=Aptamers as therapeutics |journal=Nature Reviews Drug Discovery |volume=9 |pages=537–550 |doi=10.1038/nrd3141}}</ref>, [[drug delivery systems]]<ref>{{cite journal |last1=Jiehua |first1=Zhou |last2=Rossi |first2=John |title=Cell-specific aptamer-mediated targeted drug delivery |journal=Oligonucleotides |date=2011 |doi=10.1089/oli.2010.0264}}</ref> and [[modified-release dosage|controlled drug release systems]]<ref>{{cite journal |last1=Farokhzad |first1=Omid |last2=Karp |first2=Jeffrey |last3=Langer |first3=Robert |title=Nanoparticle-aptamer bioconjugates for cancer targeting |journal=Expert opinion on drug delivery |date=2006 |doi=10.1517/17425247.3.3.311}}</ref>. They also find use in other [[molecular engineering]] tasks<ref>{{cite journal |last1=Lin |first1=Yun |last2=Jayasena |first2=Sumedha |title=Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer |journal=Journal of molecular biology |date=1997 |doi=10.1006/jmbi.1997.1165}}</ref>.
+Researchers often want aptamers that show [[sensitivity and specificity|specific and sensitive]] binding to the chosen target; resist [[hydrolysis|digestion]] by [[nucleases|DNA- and RNA-destroying proteins]]; [[clearance (pharmacology)|clear slowly from the body]]<ref>{{cite journal |last1=Wang |first1=R.E. |title=Improving the Stability of Aptamers by Chemical Modification |journal=Current Medicinal Chemistry |date=2011 |volume=18 |issue=27 |pages=4126–4138 |doi=10.2174/092986711797189565}}</ref>; [[conformational change|change their shape dramatically when they bind their target]]<ref>{{cite journal |last1=Feagin |first1=Trevor |last2=Maganzini |first2=Nicolò |last3=Soh |first3=Hyongsok |title=Strategies for Creating Structure-Switching Aptamers |journal=ACS Sensors |year=2018 |volume=3 |issue=9 |pages=1611–1615 |doi=10.1021/acssensors.8b00516|pmid=30156834 |s2cid=52120961 }}</ref>; fit into a [[biosensor]] or in a [[assay|test of a biological sample]]<ref>{{cite journal |last1=Song |first1=Shiping |title=Aptamer-based biosensors |journal=TrAC Trends in Analytical Chemistry |date=2008 |volume=27 |issue=2 |pages=108–117 |doi=10.1016/j.trac.2007.12.004 |url=https://www.sciencedirect.com/science/article/pii/S0165993607002658}}</ref>; have pre-defined [[equilibrium constant|levels]] or [[rate constant|speeds]] of binding; and are small and cheap to make. To highlight how they are similar to and different from antibodies, aptamers are sometimes called “[[antibody mimetic|chemical antibodies]].” Aptamers and antibodies can be used in many of the same tasks, but the [[nucleic acid]]-based structure of aptamers, which are mostly [[oligonucleotides]], is very different from the [[amino acid]]-based structure of antibodies, which are [[proteins]]. This difference can make aptamers a better choice than antibodies for some purposes (see [[Aptamer#Antibody_replacement|antibody replacement]]). Aptamers are used in biological lab research and clinical tests<ref>{{cite journal |last1=Tombelli |first1=Sara |last2=Minunni |first2=Maria |last3=Mascini |first3=Marco |title=Aptamers-based assays for diagnostics, environmental and food analysis |journal=Biomolecular Engineering |date=2007 |volume=24 |issue=2 |pages=191–200 |doi=10.1016/j.bioeng.2007.03.003|pmid=17434340 }}</ref>, can [[proteomics|measure large numbers of different proteins in a sample]];  [[biomarker discovery|identify molecular markers of disease]]<ref>{{cite journal |last1=Huang |first1=Jie |title=Advances in aptamer-based biomarker discovery |journal=Frontiers in Cell and Developmental Biology |date=2021 |volume=9 |page=659760 |doi=10.3389/fcell.2021.659760|pmid=33796540 |pmc=8007916 |doi-access=free }}</ref>, or function as [[RNA therapeutics|drugs]]<ref>{{cite journal |last1=Keefe |first1=Anthony |last2=Pai |first2=Supriya |last3=Ellington |first3=Andrew |title=Aptamers as therapeutics |journal=Nature Reviews Drug Discovery |year=2010 |volume=9 |issue=7 |pages=537–550 |doi=10.1038/nrd3141|pmid=20592747 |pmc=7097324 }}</ref>, [[drug delivery systems]]<ref>{{cite journal |last1=Jiehua |first1=Zhou |last2=Rossi |first2=John |title=Cell-specific aptamer-mediated targeted drug delivery |journal=Oligonucleotides |date=2011 |volume=21 |issue=1 |pages=1–10 |doi=10.1089/oli.2010.0264|pmid=21182455 |pmc=3043981 }}</ref> and [[modified-release dosage|controlled drug release systems]]<ref>{{cite journal |last1=Farokhzad |first1=Omid |last2=Karp |first2=Jeffrey |last3=Langer |first3=Robert |title=Nanoparticle-aptamer bioconjugates for cancer targeting |journal=Expert Opinion on Drug Delivery |date=2006 |volume=3 |issue=3 |pages=311–324 |doi=10.1517/17425247.3.3.311|s2cid=37058942 }}</ref>. They also find use in other [[molecular engineering]] tasks<ref>{{cite journal |last1=Lin |first1=Yun |last2=Jayasena |first2=Sumedha |title=Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer |journal=Journal of Molecular Biology |date=1997 |volume=271 |pages=100–111 |doi=10.1006/jmbi.1997.1165|pmid=9300057 }}</ref>.
-The first SELEX experiments were performed independently in 1990 by the Gold and [[Jack W. Szostak|Szostak]] labs<ref>{{cite journal |last1=Gold |first1=Larry |title=SELEX: How it happened and where it will go |journal=Journal of Molecular Evolution |date=2015 |doi=10.1007/s00239-015-9705-9}}</ref>. Commercial products and companies based on aptamers include the drug [[pegaptanib|Macugen (pegaptanib)]]<ref>{{cite web |title=FDA Approves Eyetech/Pfizer’s Macugen |url=https://www.reviewofophthalmology.com/article/fda-approves-eyetechpfizers-macugen |website=Review of Opthamology |access-date=30 June 2022}}</ref> and the [[medical diagnosis|clinical diagnostic]] company [[SomaLogic]]<ref>{{cite web |last1=Dutt |first1=Sreetama |title=SomaLogic and Illumina Combine Strengths to Propel Innovation in Proteomics |website=BioSpace |url=https://www.biospace.com/article/somalogic-and-illumina-combine-strengths-to-propel-innovation-in-proteomics-/ |access-date=30 June 2022}}</ref>. The [http://aptamersociety.org/ International Society on Aptamers (INSOAP)], a professional society for the aptamer research community, publishes a [[academic journal|journal]] devoted to the topic, ''[http://libpubmedia.co.uk/aptamers-the-official-insoap-journal/ Aptamers]''. [https://www.aptagen.com/apta-index/ Apta-index] is a current database cataloging and simplifying the ordering process for over 700 aptamers.
+The first SELEX experiments were performed independently in 1990 by the Gold and [[Jack W. Szostak|Szostak]] labs<ref>{{cite journal |last1=Gold |first1=Larry |title=SELEX: How it happened and where it will go |journal=Journal of Molecular Evolution |date=2015 |volume=81 |issue=5–6 |pages=140–143 |doi=10.1007/s00239-015-9705-9|pmid=26480964 |pmc=4661202 |bibcode=2015JMolE..81..140G }}</ref>. Commercial products and companies based on aptamers include the drug [[pegaptanib|Macugen (pegaptanib)]]<ref>{{cite web |title=FDA Approves Eyetech/Pfizer's Macugen |url=https://www.reviewofophthalmology.com/article/fda-approves-eyetechpfizers-macugen |website=Review of Opthamology |access-date=30 June 2022}}</ref> and the [[medical diagnosis|clinical diagnostic]] company [[SomaLogic]]<ref>{{cite web |last1=Dutt |first1=Sreetama |title=SomaLogic and Illumina Combine Strengths to Propel Innovation in Proteomics |website=BioSpace |url=https://www.biospace.com/article/somalogic-and-illumina-combine-strengths-to-propel-innovation-in-proteomics-/ |access-date=30 June 2022}}</ref>. The [http://aptamersociety.org/ International Society on Aptamers (INSOAP)], a professional society for the aptamer research community, publishes a [[academic journal|journal]] devoted to the topic, ''[http://libpubmedia.co.uk/aptamers-the-official-insoap-journal/ Aptamers]''. [https://www.aptagen.com/apta-index/ Apta-index] is a current database cataloging and simplifying the ordering process for over 700 aptamers.
 ==Etymology==
-The word "aptamer" is a [[neologism]] coined by Andrew Ellington and Jack Szostak in their first publication on the topic. They did not provide a precise definition, stating "We have termed these individual RNA sequences 'aptamers', from the [[Latin]] 'aptus', to fit."<ref>{{cite journal |last1=Ellington |first1=Andrew |last2=Szostak |first2=Jack |title=In vitro selection of RNA molecules that bind specific ligands |journal=Nature |date=1990 |doi=10.1038/346818a0}}</ref>. Aptamers are occasionally referred to as [[antibody mimetic|"chemical antibodies" or "antibody mimics"]]<ref>{{cite journal |last1=Gang |first1=Zhou |title=Aptamers: A promising chemical antibody for cancer therapy |journal=Oncotarget |date=2016 |doi=10.18632/oncotarget.7178}}</ref>.
+The word "aptamer" is a [[neologism]] coined by Andrew Ellington and Jack Szostak in their first publication on the topic. They did not provide a precise definition, stating "We have termed these individual RNA sequences 'aptamers', from the [[Latin]] 'aptus', to fit."<ref>{{cite journal |last1=Ellington |first1=Andrew |last2=Szostak |first2=Jack |title=In vitro selection of RNA molecules that bind specific ligands |journal=Nature |date=1990 |volume=346 |issue=6287 |pages=818–822 |doi=10.1038/346818a0|pmid=1697402 |bibcode=1990Natur.346..818E |s2cid=4273647 }}</ref>. Aptamers are occasionally referred to as [[antibody mimetic|"chemical antibodies" or "antibody mimics"]]<ref>{{cite journal |last1=Gang |first1=Zhou |title=Aptamers: A promising chemical antibody for cancer therapy |journal=Oncotarget |date=2016 |volume=7 |issue=12 |pages=13446–13463 |doi=10.18632/oncotarget.7178|pmid=26863567 |s2cid=16618423 }}</ref>.
-Researchers have coined many related labels and brand names, including "[[Spiegelmer]]," "SOMAmer," "[[smart ligand|smart aptamer]]," "[[optimer]]," "X-aptamer," "Raptamer," "aptabody," "[[affimer]]," and "[[peptide nucleic acid|peptide aptamer]]." No formal definition exists to exclude aptamers from non-aptamers, but the typical use is to describe a synthetically generated, nucleic acid-based [[ligand]] that is specific and sensitive for a particular target molecule.<ref>{{cite journal |last1=Joyce |first1=Gerald |title=In vitro evolution of nucleic acids |journal=Current opinion in structural biology |date=1994 |doi=10.1016/S0959-440X(94)90100-7}}</ref>
+Researchers have coined many related labels and brand names, including "[[Spiegelmer]]," "SOMAmer," "[[smart ligand|smart aptamer]]," "[[optimer]]," "X-aptamer," "Raptamer," "aptabody," "[[affimer]]," and "[[peptide nucleic acid|peptide aptamer]]." No formal definition exists to exclude aptamers from non-aptamers, but the typical use is to describe a synthetically generated, nucleic acid-based [[ligand]] that is specific and sensitive for a particular target molecule.<ref>{{cite journal |last1=Joyce |first1=Gerald |title=In vitro evolution of nucleic acids |journal=Current Opinion in Structural Biology |date=1994 |volume=4 |issue=3 |pages=331–336 |doi=10.1016/S0959-440X(94)90100-7|pmid=11539574 }}</ref>
 ==History==
 [[File:Jack wiki photo.jpg|thumb|150 px|[[Jack Szostak]], Nobel laureate and one of the inventors of SELEX and aptamers.]]
-The notion of selection ''in vitro'' or "directed evolution" had its roots in 1967, when [[Sol Spiegelman]] used a [[Bacteriophage Qβ|Qbeta]] replication system as a way to evolve a self-replicating molecule.<ref>{{cite journal | vauthors = Mills DR, Peterson RL, Spiegelman S | title = An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 58 | issue = 1 | pages = 217–24 | date = July 1967 | pmid = 5231602 | pmc = 335620 | doi = 10.1073/pnas.58.1.217 | bibcode = 1967PNAS...58..217M | doi-access = free }}</ref> In the ensuing decades, directed evolution was used to develop new functions in a range of bacterial proteins<ref>{{cite journal |last1=Francis |first1=J.C. |last2=Hansche |first2=P.E. |title=DIRECTED EVOLUTION OF METABOLIC PATHWAYS IN MICROBIAL POPULATIONS. I. MODIFICATION OF THE ACID PHOSPHATASE pH OPTIMUM IN S. CEREVISIAE |journal=Genetics |date=1 January 1972 |url=https://academic.oup.com/genetics/article/70/1/59/5990126?login=true}}</ref><ref>{{cite journal |last1=Hall |first1=Barry |title=Changes in the substrate specificities of an enzyme during directed evolution of new functions. |journal=Biochemistry |date=1981 |doi=10.1021/bi00517a015}}</ref>. A year before the publishing of the first SELEX and aptamers, [[Gerald Joyce]] used directed evolution to alter the cleavage activity of a [[ribozyme]]<ref>{{cite journal |last1=Joyce |first1=Gerald |title=Amplification, mutation and selection of catalytic RNA |journal=Gene |date=1989 |url=https://www.sciencedirect.com/science/article/pii/0378111989900334}}</ref>.
+The notion of selection ''in vitro'' or "directed evolution" had its roots in 1967, when [[Sol Spiegelman]] used a [[Bacteriophage Qβ|Qbeta]] replication system as a way to evolve a self-replicating molecule.<ref>{{cite journal | vauthors = Mills DR, Peterson RL, Spiegelman S | title = An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 58 | issue = 1 | pages = 217–24 | date = July 1967 | pmid = 5231602 | pmc = 335620 | doi = 10.1073/pnas.58.1.217 | bibcode = 1967PNAS...58..217M | doi-access = free }}</ref> In the ensuing decades, directed evolution was used to develop new functions in a range of bacterial proteins<ref>{{cite journal |last1=Francis |first1=J.C. |last2=Hansche |first2=P.E. |title=DIRECTED EVOLUTION OF METABOLIC PATHWAYS IN MICROBIAL POPULATIONS. I. MODIFICATION OF THE ACID PHOSPHATASE pH OPTIMUM IN S. CEREVISIAE |journal=Genetics |date=1 January 1972 |doi=10.1093/genetics/70.1.59 |pmid=4552227 |url=https://academic.oup.com/genetics/article/70/1/59/5990126?login=true}}</ref><ref>{{cite journal |last1=Hall |first1=Barry |title=Changes in the substrate specificities of an enzyme during directed evolution of new functions. |journal=Biochemistry |date=1981 |volume=20 |issue=14 |pages=4042–4049 |doi=10.1021/bi00517a015|pmid=6793063 }}</ref>. A year before the publishing of the first SELEX and aptamers, [[Gerald Joyce]] used directed evolution to alter the cleavage activity of a [[ribozyme]]<ref>{{cite journal |last1=Joyce |first1=Gerald |title=Amplification, mutation and selection of catalytic RNA |journal=Gene |date=1989 |volume=82 |pages=83–87 |doi=10.1016/0378-1119(89)90033-4 |url=https://dx.doi.org/10.1016/0378-1119%2889%2990033-4}}</ref>.
-In 1990, two labs independently developed SELEX and generated RNA aptamers: the Gold lab, using the term SELEX for their process of selecting RNA [[ligand (biochemistry)|ligands]] against T4 [[DNA polymerase]]<ref>{{cite journal |last1=Tuerk |first1=Craig |last2=Gold |first2=Larry |title=Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase |journal=Science |date=1990 |doi=10.1126/science.2200121}}</ref>; and the Szostak lab, selecting RNA ligands against various [[organic dye|organic dyes]]<ref>{{cite journal |last1=Ellington |first1=Andrew |last2=Szostak |first2=Jack |title=In vitro selection of RNA molecules that bind specific ligands |journal=Nature |date=1990 |url=https://www.nature.com/articles/346818a0}}</ref><ref>{{cite journal |last1=Stoltenburg |first1=Regina |last2=Strehlitz |first2=Beate |title=SELEX—a (r) evolutionary method to generate high-affinity nucleic acid ligands. |journal=Biomolecular engineering |date=2007 |url=https://www.sciencedirect.com/science/article/pii/S1389034407000664}}</ref>. Two years later, the Szostak lab and [[Gilead Sciences]], acting independently of one another, used ''in vitro'' selection schemes to generate DNA aptamers for organic dyes<ref>{{cite journal |last1=Ellington |first1=Andrew |last2=Szostak |first2=Jack |title=Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures |journal=Nature |date=1992 |url=https://www.nature.com/articles/355850a0}}</ref> and human [[thrombin]]<ref>{{cite journal |last1=Bock |first1=Louis |title=Selection of single-stranded DNA molecules that bind and inhibit human thrombin |journal=Nature |date=1992 |url=https://www.nature.com/articles/355564a0}}</ref> (see [[anti-thrombin aptamers]]), respectively. In 2001, SELEX was automated by J. Colin Cox in the Ellington lab, reducing the duration of a selection experiment from a time-intensive process lasting several weeks to three days<ref name="Cox2001">{{cite journal | vauthors = Cox JC, Ellington AD | title = Automated selection of anti-protein aptamers | journal = Bioorganic & Medicinal Chemistry | volume = 9 | issue = 10 | pages = 2525–31 | date = October 2001 | pmid = 11557339 | doi = 10.1016/s0968-0896(01)00028-1 }}</ref><ref name="Cox2002a">
+In 1990, two labs independently developed SELEX and generated RNA aptamers: the Gold lab, using the term SELEX for their process of selecting RNA [[ligand (biochemistry)|ligands]] against T4 [[DNA polymerase]]<ref>{{cite journal |last1=Tuerk |first1=Craig |last2=Gold |first2=Larry |title=Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase |journal=Science |date=1990 |volume=249 |issue=4968 |pages=505–510 |doi=10.1126/science.2200121|pmid=2200121 |bibcode=1990Sci...249..505T }}</ref>; and the Szostak lab, selecting RNA ligands against various [[organic dye|organic dyes]]<ref>{{cite journal |last1=Ellington |first1=Andrew |last2=Szostak |first2=Jack |title=In vitro selection of RNA molecules that bind specific ligands |journal=Nature |date=1990 |volume=346 |issue=6287 |pages=818–822 |doi=10.1038/346818a0 |bibcode=1990Natur.346..818E |s2cid=4273647 |url=https://www.nature.com/articles/346818a0}}</ref><ref>{{cite journal |last1=Stoltenburg |first1=Regina |last2=Strehlitz |first2=Beate |title=SELEX—a (r) evolutionary method to generate high-affinity nucleic acid ligands. |journal=Biomolecular Engineering |date=2007 |volume=24 |issue=4 |pages=381–403 |doi=10.1016/j.bioeng.2007.06.001 |pmid=17627883 |url=https://www.sciencedirect.com/science/article/pii/S1389034407000664}}</ref>. Two years later, the Szostak lab and [[Gilead Sciences]], acting independently of one another, used ''in vitro'' selection schemes to generate DNA aptamers for organic dyes<ref>{{cite journal |last1=Ellington |first1=Andrew |last2=Szostak |first2=Jack |title=Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures |journal=Nature |date=1992 |volume=355 |issue=6363 |pages=850–852 |doi=10.1038/355850a0 |pmid=1538766 |bibcode=1992Natur.355..850E |s2cid=4332485 |url=https://www.nature.com/articles/355850a0}}</ref> and human [[thrombin]]<ref>{{cite journal |last1=Bock |first1=Louis |title=Selection of single-stranded DNA molecules that bind and inhibit human thrombin |journal=Nature |date=1992 |volume=355 |issue=6360 |pages=564–566 |doi=10.1038/355564a0 |pmid=1741036 |bibcode=1992Natur.355..564B |s2cid=4349607 |url=https://www.nature.com/articles/355564a0}}</ref> (see [[anti-thrombin aptamers]]), respectively. In 2001, SELEX was automated by J. Colin Cox in the Ellington lab, reducing the duration of a selection experiment from a time-intensive process lasting several weeks to three days<ref name="Cox2001">{{cite journal | vauthors = Cox JC, Ellington AD | title = Automated selection of anti-protein aptamers | journal = Bioorganic & Medicinal Chemistry | volume = 9 | issue = 10 | pages = 2525–31 | date = October 2001 | pmid = 11557339 | doi = 10.1016/s0968-0896(01)00028-1 }}</ref><ref name="Cox2002a">
 {{cite journal | vauthors = Cox JC, Rajendran M, Riedel T, Davidson EA, Sooter LJ, Bayer TS, Schmitz-Brown M, Ellington AD | display-authors = 6 | title = Automated acquisition of aptamer sequences | journal = Combinatorial Chemistry & High Throughput Screening | volume = 5 | issue = 4 | pages = 289–99 | date = June 2002 | pmid = 12052180 | doi = 10.2174/1386207023330291 }}</ref><ref name="Cox2002b">
 {{cite journal | vauthors = Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, Ellington AD | title = Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer | journal = Nucleic Acids Research | volume = 30 | issue = 20 | pages = 108e–108 | date = October 2002 | pmid = 12384610 | pmc = 137152 | doi = 10.1093/nar/gnf107 }}</ref>.
-In 2002, two groups led by [[Ronald Breaker]] and Evgeny Nudler published the first comprehensive proofs of a [[riboswitch]], a nucleic acid-based [[Regulation of gene expression|genetic regulatory element]], the existence of which had previously been suspected. Riboswitches possess similar molecular recognition properties to aptamers. In addition to the discovery of a new mode of genetic regulation, this added support to the '[[RNA world hypothesis|RNA World hypothesis]]', a postulated stage in time in the [[origin of life on Earth]]<ref>{{cite journal |last1=Breaker |first1=Ronald |title=Riboswitches and the RNA world |journal=Cold Spring Harbor perspectives in biology |date=2012 |url=https://cshperspectives.cshlp.org/content/4/2/a003566.short}}</ref>.
+In 2002, two groups led by [[Ronald Breaker]] and Evgeny Nudler published the first comprehensive proofs of a [[riboswitch]], a nucleic acid-based [[Regulation of gene expression|genetic regulatory element]], the existence of which had previously been suspected. Riboswitches possess similar molecular recognition properties to aptamers. In addition to the discovery of a new mode of genetic regulation, this added support to the '[[RNA world hypothesis|RNA World hypothesis]]', a postulated stage in time in the [[origin of life on Earth]]<ref>{{cite journal |last1=Breaker |first1=Ronald |title=Riboswitches and the RNA world |journal=Cold Spring Harbor Perspectives in Biology |date=2012 |volume=4 |issue=2 |pages=a003566 |doi=10.1101/cshperspect.a003566 |pmid=21106649 |pmc=3281570 |url=https://cshperspectives.cshlp.org/content/4/2/a003566.short}}</ref>.
 ==Properties==
@@ Line 36: / Line 36: @@
 Most aptamers are based on a specific oligomer sequence of 20-100 [[nucleotide|bases]] and 3-20 [[Dalton (unit)|kDa]]. Some have chemical modifications for functional enhancements or compatibility with larger engineered molecular systems. DNA, RNA, [[Xeno nucleic acid|XNA]], and peptide aptamer chemistries can each offer distinct profiles in terms of shelf stability, durability in [[Serum (blood)|serum]] or ''[[In vivo|in vivo]]'', specificity and sensitivity, cost, ease of generation, amplification, and characterization, and familiarity to users. Typically, nucleic acid aptamers exhibit low [[immunogenicity]], are amplifiable via [[PCR]], and have complex [[Nucleic acid secondary structure|secondary structure]] and [[Nucleic acid tertiary structure|tertiary structure]]<ref>{{cite journal | vauthors = Svigelj R, Dossi N, Toniolo R, Miranda-Castro R, de-Los-Santos-Álvarez N, Lobo-Castañón MJ | title = Selection of Anti-gluten DNA Aptamers in a Deep Eutectic Solvent | journal = Angewandte Chemie | volume = 57 | issue = 39 | pages = 12850–54 | date = September 2018 | pmid = 30070419 | doi = 10.1002/ange.201804860 | bibcode = 2018AngCh.13013032S | hdl = 10651/49996 | s2cid = 240281828 }}</ref><ref>{{cite journal | vauthors = Neves MA, Reinstein O, Saad M, Johnson PE | title = Defining the secondary structural requirements of a cocaine-binding aptamer by a thermodynamic and mutation study | journal = Biophysical Chemistry | volume = 153 | issue = 1 | pages = 9–16 | date = December 2010 | pmid = 21035241 | doi = 10.1016/j.bpc.2010.09.009 }}</ref><ref>{{cite journal | vauthors = Baugh C, Grate D, Wilson C | title = 2.8 A crystal structure of the malachite green aptamer | journal = Journal of Molecular Biology | volume = 301 | issue = 1 | pages = 117–28 | date = August 2000 | pmid = 10926496 | doi = 10.1006/jmbi.2000.3951 }}</ref><ref>{{cite journal | vauthors = Dieckmann T, Fujikawa E, Xhao X, Szostak J, Feigon J |title=Structural Investigations of RNA and DNA aptamers in Solution |journal=Journal of Cellular Biochemistry |year=1995 |pages=13–81 |volume=59 |doi=10.1002/jcb.240590703 |s2cid=221833821 }}</ref>. DNA- and XNA-based aptamers exhibit superior shelf stability. XNA-based aptamers can introduce additional chemical diversity to increase binding affinity or greater durability in serum or ''in vivo''. As 22 genetically-encoded and over 500 naturally-occurring [[amino acids]] exist, relative to the 4 nucleic acids in DNA or RNA, peptide aptamers, as well as antibodies, have much greater potential combinatorial diversity per unit length. It is, however, unclear to what extent this matters for practical purposes. Chemical modifications of nucleic acid bases or backbones increase the chemical diversity of standard nucleic acid bases. The unique structure of aptamer and target shapes [[non-covalent interaction|non-covalent interactions]] between the two molecules and causes their [[Complementarity (molecular biology)|selective binding]], including via [[electrostatic]] interactions, [[hydrophobic]] interactions, [[pi stacking]], and [[hydrogen bonding]].
-Split aptamers are composed of two or more DNA strands that are pieces of a larger parent aptamer that has been broken in two by a molecular [[Nick (DNA)|nick]]<ref>{{cite journal |last1=Chen |first1=Ailiang |last2=Yan |first2=Mengmeng |last3=Yang |first3=Shuming |title=Split aptamers and their applications in sandwich aptasensors |journal=TrAC Trends in Analytical Chemistry |date=2016 |url=https://www.sciencedirect.com/science/article/pii/S0165993615301989}}</ref>. The ability of each component strand to bind targets will depend on the location of the nick, as well as the secondary structures of the daughter strands.<ref>{{cite journal | vauthors = Kent AD, Spiropulos NG, Heemstra JM | title = General approach for engineering small-molecule-binding DNA split aptamers | journal = Analytical Chemistry | volume = 85 | issue = 20 | pages = 9916–23 | date = October 2013 | pmid = 24033257 | doi = 10.1021/ac402500n }}</ref> The presence of a target molecule supports the DNA fragments joining together. This can be used as the basis for biosensors<ref>{{cite journal | vauthors = Debiais M, Lelievre A, Smietana M, Müller S | title = Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors | journal = Nucleic Acids Research | volume = 48 | issue = 7 | pages = 3400–22 | date = April 2020 | pmid = 32112111 | pmc = 7144939 | doi = 10.1093/nar/gkaa132 }}</ref>. Once assembled, the two separate DNA strands can be [[Ligation (molecular biology)|ligated]] into a single strand.
+Split aptamers are composed of two or more DNA strands that are pieces of a larger parent aptamer that has been broken in two by a molecular [[Nick (DNA)|nick]]<ref>{{cite journal |last1=Chen |first1=Ailiang |last2=Yan |first2=Mengmeng |last3=Yang |first3=Shuming |title=Split aptamers and their applications in sandwich aptasensors |journal=TrAC Trends in Analytical Chemistry |date=2016 |volume=80 |pages=581–593 |doi=10.1016/j.trac.2016.04.006 |url=https://www.sciencedirect.com/science/article/pii/S0165993615301989}}</ref>. The ability of each component strand to bind targets will depend on the location of the nick, as well as the secondary structures of the daughter strands.<ref>{{cite journal | vauthors = Kent AD, Spiropulos NG, Heemstra JM | title = General approach for engineering small-molecule-binding DNA split aptamers | journal = Analytical Chemistry | volume = 85 | issue = 20 | pages = 9916–23 | date = October 2013 | pmid = 24033257 | doi = 10.1021/ac402500n }}</ref> The presence of a target molecule supports the DNA fragments joining together. This can be used as the basis for biosensors<ref>{{cite journal | vauthors = Debiais M, Lelievre A, Smietana M, Müller S | title = Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors | journal = Nucleic Acids Research | volume = 48 | issue = 7 | pages = 3400–22 | date = April 2020 | pmid = 32112111 | pmc = 7144939 | doi = 10.1093/nar/gkaa132 }}</ref>. Once assembled, the two separate DNA strands can be [[Ligation (molecular biology)|ligated]] into a single strand.
 Non-modified aptamers are cleared rapidly from the [[bloodstream]], with a [[half-life]] of seconds to hours. This is mainly due to [[nuclease]] degradation, which physically destroys the aptamers; as well as clearance by the [[kidneys]], a result of the aptamer's low [[molecular weight]]. Several modifications, such as 2'-fluorine-substituted [[pyrimidines]] and [[polyethylene glycol]] (PEG) linkage, permit a serum half-life of days to weeks. [[PEGylation]] can add sufficient mass to prevent cleareance by the kidneys ''in vivo''. Unmodified aptamers can treat transient conditions such as [[blood clotting]], or organs such as the [[eye]] where the aptamer can be delivered without passing through the aptamer-destroying and -clearing serum. Rapid clearance from serum can also be useful in some applications, such as ''in vivo'' [[diagnostic imaging]].
@@ Line 43: / Line 43: @@
 Aptamer targets can include small molecules and heavy metal ions, larger ligands such as proteins, and even whole cells.<ref name="Nanomaterial based aptasensors for">{{cite journal | vauthors = Kaur H, Shorie M |title=Nanomaterial based aptasensors for clinical and environmental diagnostic applications |journal=Nanoscale Advances |year=2019 |volume=1 |issue=6 |pages=2123–38 |doi=10.1039/C9NA00153K |bibcode=2019NanoA...1.2123K |doi-access=free }}</ref><ref>{{cite journal | vauthors = Mallikaratchy P | title = Evolution of Complex Target SELEX to Identify Aptamers against Mammalian Cell-Surface Antigens | journal = Molecules | volume = 22 | issue = 2 | pages = 215 | date = January 2017 | pmid = 28146093 | pmc = 5572134 | doi = 10.3390/molecules22020215 | url = https://academicworks.cuny.edu/cgi/viewcontent.cgi?referer=&httpsredir=1&article=1186&context=le_pubs | doi-access = free }}</ref>. These targets include [[lysozyme]],<ref>{{cite journal | vauthors = Potty AS, Kourentzi K, Fang H, Jackson GW, Zhang X, Legge GB, Willson RC | title = Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor | journal = Biopolymers | volume = 91 | issue = 2 | pages = 145–56 | date = February 2009 | pmid = 19025993 | doi = 10.1002/bip.21097 | s2cid = 23670 }}</ref> [[thrombin]],<ref>{{cite journal | vauthors = Long SB, Long MB, White RR, Sullenger BA | title = Crystal structure of an RNA aptamer bound to thrombin | journal = RNA | volume = 14 | issue = 12 | pages = 2504–12 | date = December 2008 | pmid = 18971322 | pmc = 2590953 | doi = 10.1261/rna.1239308 }}</ref> human immunodeficiency virus [[Trans-activation response element (TAR)|trans-acting responsive element]] ([[HIV]] TAR),<ref>{{cite journal | vauthors = Darfeuille F, Reigadas S, Hansen JB, Orum H, Di Primo C, Toulmé JJ | title = Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides | journal = Biochemistry | volume = 45 | issue = 39 | pages = 12076–82 | date = October 2006 | pmid = 17002307 | doi = 10.1021/bi0606344 }}</ref> [[hemin]],<ref>{{cite journal | vauthors = Liu M, Kagahara T, Abe H, Ito Y |title=Direct In Vitro Selection of Hemin-Binding DNA Aptamer with Peroxidase Activity |journal=Bulletin of the Chemical Society of Japan |year=2009 |volume=82 |pages=99–104 |doi=10.1246/bcsj.82.99}}</ref> [[interferon γ]],<ref>{{cite journal | vauthors = Min K, Cho M, Han SY, Shim YB, Ku J, Ban C | title = A simple and direct electrochemical detection of interferon-gamma using its RNA and DNA aptamers | journal = Biosensors & Bioelectronics | volume = 23 | issue = 12 | pages = 1819–24 | date = July 2008 | pmid = 18406597 | doi = 10.1016/j.bios.2008.02.021 }}</ref> [[vascular endothelial growth factor]] (VEGF),<ref>{{cite journal | vauthors = Ng EW, Shima DT, Calias P, Cunningham ET, Guyer DR, Adamis AP | title = Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease | journal = Nature Reviews. Drug Discovery | volume = 5 | issue = 2 | pages = 123–32 | date = February 2006 | pmid = 16518379 | doi = 10.1038/nrd1955 | s2cid = 8833436 }}</ref> [[prostate specific antigen]] (PSA),<ref>{{cite journal | vauthors = Savory N, Abe K, Sode K, Ikebukuro K | title = Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing | journal = Biosensors & Bioelectronics | volume = 26 | issue = 4 | pages = 1386–91 | date = December 2010 | pmid = 20692149 | doi = 10.1016/j.bios.2010.07.057 }}</ref><ref>{{cite journal | vauthors = Jeong S, Han SR, Lee YJ, Lee SW | title = Selection of RNA aptamers specific to active prostate-specific antigen | journal = Biotechnology Letters | volume = 32 | issue = 3 | pages = 379–85 | date = March 2010 | pmid = 19943183 | doi = 10.1007/s10529-009-0168-1 | s2cid = 22201181 }}</ref> [[dopamine]],<ref>{{cite journal | vauthors = Walsh R, DeRosa MC | title = Retention of function in the DNA homolog of the RNA dopamine aptamer | journal = Biochemical and Biophysical Research Communications | volume = 388 | issue = 4 | pages = 732–35 | date = October 2009 | pmid = 19699181 | doi = 10.1016/j.bbrc.2009.08.084 }}</ref> and the non-classical oncogene, heat shock factor 1 (HSF1).<ref>{{cite journal | vauthors = Salamanca HH, Antonyak MA, Cerione RA, Shi H, Lis JT | title = Inhibiting heat shock factor 1 in human cancer cells with a potent RNA aptamer | journal = PLOS ONE | volume = 9 | issue = 5 | pages = e96330 | year = 2014 | pmid = 24800749 | pmc = 4011729 | doi = 10.1371/journal.pone.0096330 | bibcode = 2014PLoSO...996330S | doi-access = free }}</ref>
-Aptamers have been generated against cancer cells<ref>{{cite journal |last1=Smith |first1=Joshua |title=Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells |journal=Analytical Chemistry |date=2007 |url=https://www.tandfonline.com/doi/abs/10.1517/17425247.3.3.311 |access-date=2 July 2022}}</ref>, [[prions]]<ref>{{cite journal |last1=Proske |first1=Daniela |title=Prion-protein-specific aptamer reduces PrPSc formation |journal=ChemBioChem |date=2002 |url=https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/1439-7633(20020802)3:8%3C717::AID-CBIC717%3E3.0.CO;2-C |access-date=2 July 2022}}</ref>, bacteria<ref>{{cite journal | vauthors = Kaur H, Shorie M, Sharma M, Ganguli AK, Sabherwal P | title = Bridged Rebar Graphene functionalized aptasensor for pathogenic E. coli O78:K80:H11 detection | journal = Biosensors & Bioelectronics | volume = 98 | pages = 486–93 | date = December 2017 | pmid = 28728009 | doi = 10.1016/j.bios.2017.07.004 }}</ref>, and viruses. Viral targets of aptamers include [[influenza]] A and B viruses,<ref name=":0">{{cite journal | vauthors = Asha K, Kumar P, Sanicas M, Meseko CA, Khanna M, Kumar B | title = Advancements in Nucleic Acid Based Therapeutics against Respiratory Viral Infections | journal = Journal of Clinical Medicine | volume = 8 | issue = 1 | pages = 6 | date = December 2018 | pmid = 30577479 | pmc = 6351902 | doi = 10.3390/jcm8010006 | doi-access = free }}</ref> [[Respiratory syncytial virus]] (RSV),<ref name=":0" /> [[SARS coronavirus]] (SARS-CoV)<ref name=":0" /> and [[SARS-CoV-2]]<ref>{{cite journal | vauthors = Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G | title = A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism* | journal = Angewandte Chemie | volume = 60 | issue = 18 | pages = 10279–85 | date = April 2021 | pmid = 33683787 | pmc = 8251191 | doi = 10.1002/anie.202100316 }}</ref>.
+Aptamers have been generated against cancer cells<ref>{{cite journal |last1=Smith |first1=Joshua |title=Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells |journal=Analytical Chemistry |date=2007 |volume=3 |issue=3 |pages=311–324 |doi=10.1517/17425247.3.3.311 |pmid=16640493 |s2cid=37058942 |url=https://www.tandfonline.com/doi/abs/10.1517/17425247.3.3.311 |access-date=2 July 2022}}</ref>, [[prions]]<ref>{{cite journal |last1=Proske |first1=Daniela |title=Prion-protein-specific aptamer reduces PrPSc formation |journal=ChemBioChem |date=2002 |volume=3 |issue=8 |pages=717–725 |doi=10.1002/1439-7633(20020802)3:8<717::AID-CBIC717>3.0.CO;2-C |pmid=12203970 |s2cid=36801266 |url=https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/1439-7633(20020802)3:8%3C717::AID-CBIC717%3E3.0.CO;2-C |access-date=2 July 2022}}</ref>, bacteria<ref>{{cite journal | vauthors = Kaur H, Shorie M, Sharma M, Ganguli AK, Sabherwal P | title = Bridged Rebar Graphene functionalized aptasensor for pathogenic E. coli O78:K80:H11 detection | journal = Biosensors & Bioelectronics | volume = 98 | pages = 486–93 | date = December 2017 | pmid = 28728009 | doi = 10.1016/j.bios.2017.07.004 }}</ref>, and viruses. Viral targets of aptamers include [[influenza]] A and B viruses,<ref name=":0">{{cite journal | vauthors = Asha K, Kumar P, Sanicas M, Meseko CA, Khanna M, Kumar B | title = Advancements in Nucleic Acid Based Therapeutics against Respiratory Viral Infections | journal = Journal of Clinical Medicine | volume = 8 | issue = 1 | pages = 6 | date = December 2018 | pmid = 30577479 | pmc = 6351902 | doi = 10.3390/jcm8010006 | doi-access = free }}</ref> [[Respiratory syncytial virus]] (RSV),<ref name=":0" /> [[SARS coronavirus]] (SARS-CoV)<ref name=":0" /> and [[SARS-CoV-2]]<ref>{{cite journal | vauthors = Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G | title = A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism* | journal = Angewandte Chemie | volume = 60 | issue = 18 | pages = 10279–85 | date = April 2021 | pmid = 33683787 | pmc = 8251191 | doi = 10.1002/anie.202100316 }}</ref>.
-Aptamers may be particularly useful for [[environmental science]] proteomics<ref>{{cite journal |last1=Dhar |first1=Poshmaal |last2=Samarasinghe |first2=Rasika |last3=Shigdar |first3=Sarah |title=Antibodies, nanobodies, or aptamers—which is best for deciphering the proteomes of non-model species? |journal=International journal of molecular sciences |url=https://www.mdpi.com/1422-0067/21/7/2485 |access-date=2 July 2022}}</ref>. Antibodies, like other proteins, are more difficult to sequence than nucleic acids. They are also costly to maintain and produce, and at constant risk of contamination, as they are produced via [[cell culture]] or are harvested from animal serum. For this reason, researchers interested in little-studied proteins and species may find that companies will not produce, maintain, or validate the quality of antibodies against their target of interest.<ref>{{cite journal |last1=Bauer |first1=Michelle |title=Anything you can do, I can do better: Can aptamers replace antibodies in clinical diagnostic applications? |journal=Molecules |date=2019 |url=https://www.mdpi.com/1420-3049/24/23/4377}}</ref>. By contrast, aptamers are simple to sequence and cost nothing to maintain, as their exact structure can be stored digitally and synthesized on demand. This may make them more economically feasible as research tools for underfunded biological research subjects. Aptamers exist for plant compounds, such as [[theophylline]] (found in [[tea]])<ref>{{cite journal |last1=Feng |first1=Silu |title=An aptamer nanopore-enabled microsensor for detection of theophylline. |journal=Biosensors and Bioelectronics |date=2018 |url=https://www.sciencedirect.com/science/article/pii/S0956566318300228 |access-date=2 July 2022}}</ref> and [[abscisic acid]] (a plant immune hormone)<ref>{{cite journal |last1=Song |first1=Chao |title=Detection of plant hormone abscisic acid (ABA) using an optical aptamer-based sensor with a microfluidics capillary interface |journal=2017 IEEE 30th International Conference on Micro Electro Mechanical Systems (MEMS) |date=2017 |url=https://ieeexplore.ieee.org/abstract/document/7863418}}</ref>. An aptamer against [[a-amanitin]] (the toxin that causes lethal [[amanita]] poisoning) has been developed, an example of an aptamer against a [[mushroom]] target<ref>{{cite journal |last1=Muszyńska |first1=K. |last2=Ostrowska |first2=D. |last3=Bartnicki |first3=F. |last4=Kowalska |first4=E. |last5=Bodaszewska-Lubaś |first5=M. |last6=Hermanowicz |first6=P. |last7=Strzałka |first7=W. |title=Selection and analysis of a DNA aptamer binding α-amanitin from Amanita phalloides |journal=Acta Biochimica Polonica |url=https://www.ojs.ptbioch.edu.pl/index.php/abp/article/view/1615 |access-date=2 July 2022}}</ref>.
+Aptamers may be particularly useful for [[environmental science]] proteomics<ref>{{cite journal |last1=Dhar |first1=Poshmaal |last2=Samarasinghe |first2=Rasika |last3=Shigdar |first3=Sarah |title=Antibodies, nanobodies, or aptamers—which is best for deciphering the proteomes of non-model species? |journal=International Journal of Molecular Sciences |year=2020 |volume=21 |issue=7 |page=2485 |doi=10.3390/ijms21072485 |doi-access=free }}</ref>. Antibodies, like other proteins, are more difficult to sequence than nucleic acids. They are also costly to maintain and produce, and at constant risk of contamination, as they are produced via [[cell culture]] or are harvested from animal serum. For this reason, researchers interested in little-studied proteins and species may find that companies will not produce, maintain, or validate the quality of antibodies against their target of interest.<ref>{{cite journal |last1=Bauer |first1=Michelle |title=Anything you can do, I can do better: Can aptamers replace antibodies in clinical diagnostic applications? |journal=Molecules |date=2019 |volume=24 |issue=23 |page=4377 |doi=10.3390/molecules24234377 |pmid=31801185 |pmc=6930532 |doi-access=free }}</ref>. By contrast, aptamers are simple to sequence and cost nothing to maintain, as their exact structure can be stored digitally and synthesized on demand. This may make them more economically feasible as research tools for underfunded biological research subjects. Aptamers exist for plant compounds, such as [[theophylline]] (found in [[tea]])<ref>{{cite journal |last1=Feng |first1=Silu |title=An aptamer nanopore-enabled microsensor for detection of theophylline. |journal=Biosensors and Bioelectronics |date=2018 |volume=105 |pages=36–41 |doi=10.1016/j.bios.2018.01.016 |pmid=29351868 |url=https://www.sciencedirect.com/science/article/pii/S0956566318300228 |access-date=2 July 2022}}</ref> and [[abscisic acid]] (a plant immune hormone)<ref>{{cite journal |last1=Song |first1=Chao |title=Detection of plant hormone abscisic acid (ABA) using an optical aptamer-based sensor with a microfluidics capillary interface |journal=2017 IEEE 30th International Conference on Micro Electro Mechanical Systems (MEMS) |date=2017 |pages=370–373 |doi=10.1109/MEMSYS.2017.7863418 |isbn=978-1-5090-5078-9 |s2cid=20781208 |url=https://ieeexplore.ieee.org/document/7863418}}</ref>. An aptamer against [[a-amanitin]] (the toxin that causes lethal [[amanita]] poisoning) has been developed, an example of an aptamer against a [[mushroom]] target<ref>{{cite journal |last1=Muszyńska |first1=K. |last2=Ostrowska |first2=D. |last3=Bartnicki |first3=F. |last4=Kowalska |first4=E. |last5=Bodaszewska-Lubaś |first5=M. |last6=Hermanowicz |first6=P. |last7=Strzałka |first7=W. |title=Selection and analysis of a DNA aptamer binding α-amanitin from Amanita phalloides |journal=Acta Biochimica Polonica |url=https://www.ojs.ptbioch.edu.pl/index.php/abp/article/view/1615 |access-date=2 July 2022}}</ref>.
 ===Peptide Aptamers===
@@ Line 64: / Line 64: @@
 [[File:Aptamer gel mobility shift assay.jpg|thumb|This assay tests the ability of two different types of aptamers (V and I) to detect their respective protein targets (VEGF and IFN-y). The labels Apt1, Apt2, Apt3, and Apt4 are in decreasing order of binding strength (i.e. Apt1 is the strongest aptamer). The DD, AD, DA, and AA letters mean that they have different combinations of unnatural base pairs. This causes their difference in binding strengths. The "-" columns have no protein, and the "+" columns do have protein. Aptamer with protein (+) and without protein (-) is loaded into wells in a gel and moves down the column lanes. If target is present, they bind and travel more slowly, due to the [[ion|charge]] on the aptamer and the mass of the protein. Otherwise, the unbound aptamer moves quickly to the end of the lane. The difference in position between the "+" and "-" bands is the "mobility shift." This allows the researcher to detect the presence or absence of the protein. The darker band in the leftmost V and I lanes show that stronger aptamer-target binding makes it easier to detect the target at a given amount of target protein in the sample. The bottom image includes [[Denaturation (biochemistry)|denaturing]] [[urea]] in the gel that disrupts aptamer-target binding in the weaker I aptamers, showing that the aptamer-protein binding is indeed what caused the mobility shift.|520x212 px]]
-Aptamer applications can be roughly grouped into sensing, therapeutic, and engineering categories. Sensing applications are important in environmental, biomedical, epidemiological, biosecurity, and basic research applications, where aptamers act as probes in assays, imaging methods, diagnostic assays, and biosensors<ref name="Nanomaterial based aptasensors for"/><ref>{{Cite web |last=Penner |first=Gregory |date=July 2012 |title=Commercialization of an aptamer-based diagnostic test |website=NeoVentures |url=https://neoaptamers.com/wp-content/uploads/2021/01/Penner2012IVDTech31commercializationaptamer-baseddiagkits-1.pdf}}</ref><ref>{{cite journal | vauthors = Wei H, Li B, Li J, Wang E, Dong S | title = Simple and sensitive aptamer-based colorimetric sensing of protein using unmodified gold nanoparticle probes | journal = Chemical Communications  | issue = 36 | pages = 3735–37 | date = September 2007 | pmid = 17851611 | doi = 10.1039/B707642H }}</ref><ref>{{cite journal | vauthors = Cheng H, Qiu X, Zhao X, Meng W, Huo D, Wei H | title = Functional Nucleic Acid Probe for Parallel Monitoring K(+) and Protoporphyrin IX in Living Organisms | journal = Analytical Chemistry | volume = 88 | issue = 5 | pages = 2937–43 | date = March 2016 | pmid = 26866998 | doi = 10.1021/acs.analchem.5b04936 }}</ref><ref>{{cite journal | vauthors = Xiang Y, Lu Y | title = Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets | journal = Nature Chemistry | volume = 3 | issue = 9 | pages = 697–703 | date = July 2011 | pmid = 21860458 | pmc = 3299819 | doi = 10.1038/nchem.1092 | bibcode = 2011NatCh...3..697X }}</ref><ref>Agnivo Gosai, Brendan Shin Hau Yeah, Marit Nilsen-Hamilton, Pranav Shrotriya, "Label free thrombin detection in presence of high concentration of albumin using an aptamer-functionalized nanoporous membrane", ''Biosensors and Bioelectronics'', Volume 126, 2019, pp. 88–95, {{ISSN|0956-5663}}, {{doi|10.1016/j.bios.2018.10.010}}.</ref>. In therapeutic applications and [[precision medicine]], aptamers can function as drugs<ref>{{Cite journal|last1=Amero|first1=Paola|last2=Khatua|first2=Soumen|last3=Rodriguez-Aguayo|first3=Cristian|last4=Lopez-Berestein|first4=Gabriel|date=October 2020|title=Aptamers: Novel Therapeutics and Potential Role in Neuro-Oncology|journal=Cancers|language=en|volume=12|issue=10 |pages=2889 |doi=10.3390/cancers12102889|pmid=33050158|pmc=7600320|doi-access=free}}</ref>, targeted drug delivery vehicles<ref>{{Cite journal|last1=Fattal|first1=Elias|last2=Hillaireau|first2=Hervé |last3=Ismail|first3=Said I.|date=September 2018|title=Aptamers in Therapeutics and Drug Delivery |url=https://pubmed.ncbi.nlm.nih.gov/30442313/|journal=Advanced Drug Delivery Reviews|volume=134|pages=1–2 |doi=10.1016/j.addr.2018.11.001|issn=1872-8294|pmid=30442313|s2cid=53562925}}</ref>, as controlled release mechanisms, and as reagents for drug discovery via [[high-throughput screening]] for small molecules<ref>{{cite journal |vauthors=Hafner M, Vianini E, Albertoni B, Marchetti L, Grüne I, Gloeckner C, Famulok M |title=Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization |journal=Nature Protocols |volume=3 |issue=4 |pages=579–587 |date=2008 |pmid=18388939 |doi=10.1038/nprot.2008.15 |s2cid=4997899}}</ref> and proteins<ref>{{Cite journal|last1=Huang|first1=Zike|last2=Qiu|first2=Liping|last3=Zhang|first3=Tao|last4=Tan|first4=Weihong|date=2021-02-03|title=Integrating DNA Nanotechnology with Aptamers for Biological and Biomedical Applications|url=https://www.sciencedirect.com/science/article/pii/S2590238520306196|journal=Matter|language=en|volume=4|issue=2|pages=461–489|doi=10.1016/j.matt.2020.11.002|s2cid=234061584|issn=2590-2385}}</ref><ref>{{Cite journal|last1=Reynaud|first1=Lucile|last2=Bouchet-Spinelli|first2=Aurélie|last3=Raillon|first3=Camille|last4=Buhot|first4=Arnaud|date=January 2020|title=Sensing with Nanopores and Aptamers: A Way Forward|journal=Sensors |language=en|volume=20|issue=16|pages=4495|doi=10.3390/s20164495|pmid=32796729|pmc=7472324|bibcode=2020Senso..20.4495R|doi-access=free}}</ref>. They can function in molecular engineering applications as a way to modify proteins, such as enhancing DNA polymerase with hot start properties to make PCR more reliable<ref>{{Cite journal|last1=Keijzer|first1=Jordi F.|last2=Albada|first2=Bauke|title=DNA-assisted site-selective protein modification|journal=Biopolymers|year=2022|volume=113|issue=3|pages=e23483 |doi=10.1002/bip.23483|pmid=34878181|s2cid=244954278|issn=1097-0282}}</ref><ref>{{Cite journal|last1=Smith |first1=Drew|last2=Collins|first2=Brian D.|last3=Heil|first3=James|last4=Koch|first4=Tad H.|date=January 2003 |title=Sensitivity and Specificity of Photoaptamer Probes|journal=Molecular & Cellular Proteomics |volume=2|issue=1|pages=11–18 |doi=10.1074/mcp.m200059-mcp200 |pmid=12601078|s2cid=13406870|issn=1535-9476}}</ref><ref>{{Cite journal |last1=Vinkenborg|first1=Jan L.|last2=Mayer|first2=Günter|last3=Famulok |first3=Michael|date=2012-08-02|title=Aptamer-Based Affinity Labeling of Proteins|journal=Angewandte Chemie International Edition|volume=51|issue=36 |pages=9176–9180|doi=10.1002/anie.201204174|pmid=22865679 |issn=1433-7851}}</ref><ref>{{Cite journal|last1=Keijzer |first1=Jordi F.|last2=Firet|first2=Judith |last3=Albada|first3=Bauke|date=2021|title=Site-selective and inducible acylation of thrombin using aptamer-catalyst conjugates|journal=Chemical Communications|volume=57|issue=96|pages=12960–12963 |doi=10.1039/d1cc05446e|pmid=34792071|s2cid=243998479|issn=1359-7345}}</ref>.
+Aptamer applications can be roughly grouped into sensing, therapeutic, and engineering categories. Sensing applications are important in environmental, biomedical, epidemiological, biosecurity, and basic research applications, where aptamers act as probes in assays, imaging methods, diagnostic assays, and biosensors<ref name="Nanomaterial based aptasensors for"/><ref>{{Cite web |last=Penner |first=Gregory |date=July 2012 |title=Commercialization of an aptamer-based diagnostic test |website=NeoVentures |url=https://neoaptamers.com/wp-content/uploads/2021/01/Penner2012IVDTech31commercializationaptamer-baseddiagkits-1.pdf}}</ref><ref>{{cite journal | vauthors = Wei H, Li B, Li J, Wang E, Dong S | title = Simple and sensitive aptamer-based colorimetric sensing of protein using unmodified gold nanoparticle probes | journal = Chemical Communications  | issue = 36 | pages = 3735–37 | date = September 2007 | pmid = 17851611 | doi = 10.1039/B707642H }}</ref><ref>{{cite journal | vauthors = Cheng H, Qiu X, Zhao X, Meng W, Huo D, Wei H | title = Functional Nucleic Acid Probe for Parallel Monitoring K(+) and Protoporphyrin IX in Living Organisms | journal = Analytical Chemistry | volume = 88 | issue = 5 | pages = 2937–43 | date = March 2016 | pmid = 26866998 | doi = 10.1021/acs.analchem.5b04936 }}</ref><ref>{{cite journal | vauthors = Xiang Y, Lu Y | title = Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets | journal = Nature Chemistry | volume = 3 | issue = 9 | pages = 697–703 | date = July 2011 | pmid = 21860458 | pmc = 3299819 | doi = 10.1038/nchem.1092 | bibcode = 2011NatCh...3..697X }}</ref><ref>Agnivo Gosai, Brendan Shin Hau Yeah, Marit Nilsen-Hamilton, Pranav Shrotriya, "Label free thrombin detection in presence of high concentration of albumin using an aptamer-functionalized nanoporous membrane", ''Biosensors and Bioelectronics'', Volume 126, 2019, pp. 88–95, {{ISSN|0956-5663}}, {{doi|10.1016/j.bios.2018.10.010}}.</ref>. In therapeutic applications and [[precision medicine]], aptamers can function as drugs<ref>{{Cite journal|last1=Amero|first1=Paola|last2=Khatua|first2=Soumen|last3=Rodriguez-Aguayo|first3=Cristian|last4=Lopez-Berestein|first4=Gabriel|date=October 2020|title=Aptamers: Novel Therapeutics and Potential Role in Neuro-Oncology|journal=Cancers|language=en|volume=12|issue=10 |pages=2889 |doi=10.3390/cancers12102889|pmid=33050158|pmc=7600320|doi-access=free}}</ref>, targeted drug delivery vehicles<ref>{{Cite journal|last1=Fattal|first1=Elias|last2=Hillaireau|first2=Hervé |last3=Ismail|first3=Said I.|date=September 2018|title=Aptamers in Therapeutics and Drug Delivery |url=https://pubmed.ncbi.nlm.nih.gov/30442313/|journal=Advanced Drug Delivery Reviews|volume=134|pages=1–2 |doi=10.1016/j.addr.2018.11.001|issn=1872-8294|pmid=30442313|s2cid=53562925}}</ref>, as controlled release mechanisms, and as reagents for drug discovery via [[high-throughput screening]] for small molecules<ref>{{cite journal |vauthors=Hafner M, Vianini E, Albertoni B, Marchetti L, Grüne I, Gloeckner C, Famulok M |title=Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization |journal=Nature Protocols |volume=3 |issue=4 |pages=579–587 |date=2008 |pmid=18388939 |doi=10.1038/nprot.2008.15 |s2cid=4997899}}</ref> and proteins<ref>{{Cite journal|last1=Huang|first1=Zike|last2=Qiu|first2=Liping|last3=Zhang|first3=Tao|last4=Tan|first4=Weihong|date=2021-02-03|title=Integrating DNA Nanotechnology with Aptamers for Biological and Biomedical Applications|url=https://www.sciencedirect.com/science/article/pii/S2590238520306196|journal=Matter|language=en|volume=4|issue=2|pages=461–489|doi=10.1016/j.matt.2020.11.002|s2cid=234061584|issn=2590-2385}}</ref><ref>{{Cite journal|last1=Reynaud|first1=Lucile|last2=Bouchet-Spinelli|first2=Aurélie|last3=Raillon|first3=Camille|last4=Buhot|first4=Arnaud|date=January 2020|title=Sensing with Nanopores and Aptamers: A Way Forward|journal=Sensors |language=en|volume=20|issue=16|pages=4495|doi=10.3390/s20164495|pmid=32796729|pmc=7472324|bibcode=2020Senso..20.4495R|doi-access=free}}</ref>. They can function in molecular engineering applications as a way to modify proteins, such as enhancing DNA polymerase with hot start properties to make PCR more reliable<ref>{{Cite journal|last1=Keijzer|first1=Jordi F.|last2=Albada|first2=Bauke|title=DNA-assisted site-selective protein modification|journal=Biopolymers|year=2022|volume=113|issue=3|pages=e23483 |doi=10.1002/bip.23483|pmid=34878181|s2cid=244954278|issn=1097-0282|url=https://library.wur.nl/WebQuery/wurpubs/590725 }}</ref><ref>{{Cite journal|last1=Smith |first1=Drew|last2=Collins|first2=Brian D.|last3=Heil|first3=James|last4=Koch|first4=Tad H.|date=January 2003 |title=Sensitivity and Specificity of Photoaptamer Probes|journal=Molecular & Cellular Proteomics |volume=2|issue=1|pages=11–18 |doi=10.1074/mcp.m200059-mcp200 |pmid=12601078|s2cid=13406870|issn=1535-9476}}</ref><ref>{{Cite journal |last1=Vinkenborg|first1=Jan L.|last2=Mayer|first2=Günter|last3=Famulok |first3=Michael|date=2012-08-02|title=Aptamer-Based Affinity Labeling of Proteins|journal=Angewandte Chemie International Edition|volume=51|issue=36 |pages=9176–9180|doi=10.1002/anie.201204174|pmid=22865679 |issn=1433-7851}}</ref><ref>{{Cite journal|last1=Keijzer |first1=Jordi F.|last2=Firet|first2=Judith |last3=Albada|first3=Bauke|date=2021|title=Site-selective and inducible acylation of thrombin using aptamer-catalyst conjugates|journal=Chemical Communications|volume=57|issue=96|pages=12960–12963 |doi=10.1039/d1cc05446e|pmid=34792071|s2cid=243998479|issn=1359-7345}}</ref>.
 ===Antibody replacement===
-Aptamers can replace antibodies in many [[biotechnology]] applications<ref>{{cite journal |last1=Chen |first1=Ailiang |last2=Yang |first2=Shuming |title=Replacing antibodies with aptamers in lateral flow immunoassay |journal=Biosensors and bioelectronics |date=2015 |url=https://www.sciencedirect.com/science/article/pii/S0956566315300427}}</ref><ref>{{cite journal |last1=Bauer |first1=Michelle |title=Anything you can do, I can do better: Can aptamers replace antibodies in clinical diagnostic applications? |journal=Molecules |date=2019 |url=https://www.mdpi.com/1420-3049/24/23/4377}}</ref>. In laboratory research and clinical diagnostics, they can be used in aptamer-based versions of [[immunoassay|immunoassays]] including [[ELISA]]<ref>{{cite journal |last1=Toh |first1=Saw Yi |title=Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay |journal=Biosensors and bioelectronics |date=2015 |doi=10.1016/j.bios.2014.09.026}}</ref>, [[western blot]]<ref>{{cite journal |last1=Bruno |first1=J.G. |last2=Sivils |first2=J.C. |title=Aptamer “Western” blotting for E. coli outer membrane proteins and key virulence factors in pathogenic E. coli serotypes |journal=Aptamers and Synthetic Antibodies |date=2016 |url=http://researcherslinks.com/current-issues/Measuring-Predictive-Performance-Data-Mining-Artificial-Neural-Akkaraman-Sheep%20/20/1/234/html}}</ref>, [[immunohistochemistry|IHC]]<ref>{{cite journal |last1=Bauer |first1=Michelle |title=The application of aptamers for immunohistochemistry |journal=Nucleic acid therapeutics |date=2016 |doi=10.1089/nat.2015.0569}}</ref>, and [[flow cytometry]]<ref>{{cite journal |last1=Meyer |first1=Michael |last2=Scheper |first2=Thomas |last3=Walter |first3=Johanna-Gabriela |title=Aptamers: versatile probes for flow cytometry |journal=Applied microbiology and biotechnology |date=2013 |url=https://link.springer.com/article/10.1007/s00253-013-5070-z}}</ref>. As therapeutics, they can function as [[agonists]] or [[receptor antagonist|antagonists]] of their ligand<ref>{{cite journal |last1=Zhou |first1=Jiehua |last2=Rossi |first2=John |title=Aptamers as targeted therapeutics: current potential and challenges. |journal=Nature reviews Drug discovery |date=2017 |url=https://www.nature.com/articles/nrd.2016.199}}</ref>. While antibodies are a familiar technology with a well-developed market, aptamers are a relatively new technology to most researchers, and aptamers have been generated against only a fraction of important research targets<ref>{{cite journal |last1=Bruno |first1=John |title=Predicting the Uncertain Future of Aptamer-Based Diagnostics and Therapeutics |journal=Molecules |date=2015 |url=https://www.mdpi.com/1420-3049/20/4/6866}}</ref>. Unlike antibodies, unmodified aptamers are more susceptible to nuclease digestion in serum and renal clearance ''in vivo''. Aptamers are much smaller in size and mass than antibodies, which could be a relevant factor in choosing which is best suited for a given application. When aptamers are available for a particular application, their advantages over antibodies include potentially lower immunogenicity, greater [[replicability]] and lower cost, a greater level of control due to the ''in vitro'' selection conditions, and capacity to be efficiently engineered for durability, specificity, and sensitivity<ref>{{cite journal |last1=Wang |first1=Tao |title=Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development |journal=Biotechnology advances |date=2019 |url=https://www.sciencedirect.com/science/article/pii/S0734975018301770}}</ref>.
+Aptamers can replace antibodies in many [[biotechnology]] applications<ref>{{cite journal |last1=Chen |first1=Ailiang |last2=Yang |first2=Shuming |title=Replacing antibodies with aptamers in lateral flow immunoassay |journal=Biosensors and Bioelectronics |date=2015 |volume=71 |pages=230–242 |doi=10.1016/j.bios.2015.04.041 |pmid=25912679 |url=https://www.sciencedirect.com/science/article/pii/S0956566315300427}}</ref><ref>{{cite journal |last1=Bauer |first1=Michelle |title=Anything you can do, I can do better: Can aptamers replace antibodies in clinical diagnostic applications? |journal=Molecules |date=2019 |volume=24 |issue=23 |page=4377 |doi=10.3390/molecules24234377 |pmid=31801185 |pmc=6930532 |doi-access=free }}</ref>. In laboratory research and clinical diagnostics, they can be used in aptamer-based versions of [[immunoassay|immunoassays]] including [[ELISA]]<ref>{{cite journal |last1=Toh |first1=Saw Yi |title=Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay |journal=Biosensors and Bioelectronics |date=2015 |volume=64 |pages=392–403 |doi=10.1016/j.bios.2014.09.026|pmid=25278480 }}</ref>, [[western blot]]<ref>{{cite journal |last1=Bruno |first1=J.G. |last2=Sivils |first2=J.C. |title=Aptamer "Western" blotting for E. coli outer membrane proteins and key virulence factors in pathogenic E. coli serotypes |journal=Aptamers and Synthetic Antibodies |date=2016 |url=http://researcherslinks.com/current-issues/Measuring-Predictive-Performance-Data-Mining-Artificial-Neural-Akkaraman-Sheep%20/20/1/234/html}}</ref>, [[immunohistochemistry|IHC]]<ref>{{cite journal |last1=Bauer |first1=Michelle |title=The application of aptamers for immunohistochemistry |journal=Nucleic Acid Therapeutics |date=2016 |volume=26 |issue=3 |pages=120–126 |doi=10.1089/nat.2015.0569|pmid=26862683 }}</ref>, and [[flow cytometry]]<ref>{{cite journal |last1=Meyer |first1=Michael |last2=Scheper |first2=Thomas |last3=Walter |first3=Johanna-Gabriela |title=Aptamers: versatile probes for flow cytometry |journal=Applied Microbiology and Biotechnology |date=2013 |volume=97 |issue=16 |pages=7097–7109 |doi=10.1007/s00253-013-5070-z |pmid=23838792 |s2cid=13996688 |url=https://link.springer.com/article/10.1007/s00253-013-5070-z}}</ref>. As therapeutics, they can function as [[agonists]] or [[receptor antagonist|antagonists]] of their ligand<ref>{{cite journal |last1=Zhou |first1=Jiehua |last2=Rossi |first2=John |title=Aptamers as targeted therapeutics: current potential and challenges. |journal=Nature Reviews Drug Discovery |date=2017 |volume=16 |issue=3 |pages=181–202 |doi=10.1038/nrd.2016.199 |pmid=27807347 |pmc=5700751 }}</ref>. While antibodies are a familiar technology with a well-developed market, aptamers are a relatively new technology to most researchers, and aptamers have been generated against only a fraction of important research targets<ref>{{cite journal |last1=Bruno |first1=John |title=Predicting the Uncertain Future of Aptamer-Based Diagnostics and Therapeutics |journal=Molecules |date=2015 |volume=20 |issue=4 |pages=6866–6887 |doi=10.3390/molecules20046866 |pmid=25913927 |pmc=6272696 |doi-access=free }}</ref>. Unlike antibodies, unmodified aptamers are more susceptible to nuclease digestion in serum and renal clearance ''in vivo''. Aptamers are much smaller in size and mass than antibodies, which could be a relevant factor in choosing which is best suited for a given application. When aptamers are available for a particular application, their advantages over antibodies include potentially lower immunogenicity, greater [[replicability]] and lower cost, a greater level of control due to the ''in vitro'' selection conditions, and capacity to be efficiently engineered for durability, specificity, and sensitivity<ref>{{cite journal |last1=Wang |first1=Tao |title=Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development |journal=Biotechnology Advances |date=2019 |volume=37 |issue=1 |pages=28–50 |doi=10.1016/j.biotechadv.2018.11.001 |pmid=30408510 |s2cid=53242220 |url=https://www.sciencedirect.com/science/article/pii/S0734975018301770}}</ref>.
-In addition, aptamers contribute to [[Three Rs (animal research)|reduction of research animal use]]<ref>{{cite journal |last1=Melbourne |first1=Jodie |title=A Multi-faceted Approach to Achieving the Global Acceptance of Animal-free Research Methods |journal=Alternatives to Laboratory Animals |date=2016 |doi=10.1177/026119291604400511}}</ref>. While antibodies often rely on animals for initial discovery, as well as for production in the case of [[polyclonal antibodies]], both the selection and production of aptamers is typically animal-free. However, note that [[phage display]] methods allow for selection of antibodies [[in vitro]], followed by production from a monoclonal cell line, avoiding the use of animals entirely<ref>{{cite journal |last1=Alfaleh |first1=Mohamed A. |title=Phage display derived monoclonal antibodies: from bench to bedside |journal=Frontiers in immunology |date=1986 |url=https://www.frontiersin.org/articles/10.3389/fimmu.2020.01986/full}}</ref>.
+In addition, aptamers contribute to [[Three Rs (animal research)|reduction of research animal use]]<ref>{{cite journal |last1=Melbourne |first1=Jodie |title=A Multi-faceted Approach to Achieving the Global Acceptance of Animal-free Research Methods |journal=Alternatives to Laboratory Animals |date=2016 |volume=44 |issue=5 |pages=495–498 |doi=10.1177/026119291604400511|pmid=27805832 |s2cid=1002312 }}</ref>. While antibodies often rely on animals for initial discovery, as well as for production in the case of [[polyclonal antibodies]], both the selection and production of aptamers is typically animal-free. However, note that [[phage display]] methods allow for selection of antibodies [[in vitro]], followed by production from a monoclonal cell line, avoiding the use of animals entirely<ref>{{cite journal |last1=Alfaleh |first1=Mohamed A. |title=Phage display derived monoclonal antibodies: from bench to bedside |journal=Frontiers in Immunology |year=2020 |volume=11 |page=1986 |doi=10.3389/fimmu.2020.01986 |pmid=32983137 |pmc=7485114 |doi-access=free }}</ref>.
 === Controlled release of therapeutics ===

Aptamer: Difference between revisions

Revision as of 20:55, 3 July 2022

Etymology

History

Properties

Structure

Targets

Peptide Aptamers

Structure

Selection

Applications

Applications

Antibody replacement

Controlled release of therapeutics

PCR

AptaBiD

See also

References

Further reading