Aptamer: Difference between revisions

From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
Fix many DOIs.
Line 17: Line 17:
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 evlution 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 |url=https://pubs.acs.org/doi/pdf/10.1021/bi00517a015}}</ref>. In addition, a year before the publishing of ''in vitro selection'' and SELEX, [[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 evlution 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 |url=https://pubs.acs.org/doi/pdf/10.1021/bi00517a015}}</ref>. In addition, a year before the publishing of ''in vitro selection'' and SELEX, [[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>.


In 1990, two labs independently developed the technique of selection: the Gold lab, using the term SELEX for their process of selecting RNA [[ligand (biochemistry)|ligands]] against T4 [[DNA polymerase]]; and the Szostak lab, selecting RNA ligands against various organic dyes. Two years later, the Szostak lab and [[Gilead Sciences]], independent of one another, used ''in vitro selection'' schemes to evolve single stranded DNA ligands for organic dyes and human coagulant, thrombin (see [[anti-thrombin aptamers]]), respectively.
In 1990, two labs independently developed the technique of selection: 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 |url=https://www.science.org/doi/abs/10.1126/science.2200121}}</ref>; and the Szostak lab, selecting RNA ligands against various 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]], independent of one another, used ''in vitro selection'' schemes to evolve single stranded DNA ligands for organic dyes and human coagulant, thrombin (see [[anti-thrombin aptamers]]), respectively.


Since the discovery of aptamers, many researchers have used aptamer selection as a means for application and discovery. In 2001, the process of ''in vitro selection'' was automated<ref name="Cox2001">
Since the discovery of aptamers, many researchers have used aptamer selection as a means for application and discovery. In 2001, the process of ''in vitro selection'' was automated<ref name="Cox2001">

Revision as of 21:29, 30 June 2022

Structure of an RNA aptamer specific for biotin. The aptamer surface and backbone are shown in yellow. Biotin (spheres) fits snugly into a cavity of the RNA surface

Aptamers are oligomers, typically based on synthetic DNA or RNA sequences, that bind a specific target molecule with sensitivity and specificity comparable to or exceeding that of antibodies[1]. Natural aptamers also exist in riboswitches[2].

Most aptamers are generated by SELEX, a diverse family of primarily in vitro techniques[3]. Typically, the researcher iteratively selects for aptamers with desirable qualities from an initial "library" consisting of a massive number of distinct, randomly generated oligomers. They may mutate or chemically modify it and subject it to additional selection[4], or subject it to rational design processes to improve its qualities further[5]. Non-SELEX methods for aptamer discovery also exist[6]. Desirable properties can include specific and sensitive binding; resistance to nuclease digestion and renal clearance[7]; conformational change[8]; incorporation and detectability in an assay or biosensor[9]; pre-defined equilibrium () and rate (, ) constants as well as thermodynamic (ΔH, ΔS) parameters; and smaller size. Sometimes referred to as “chemical antibodies,” their nucleic acid structure can be advantageous for similar applications. Aptamers are used in lab and clinical assays[10], plasma proteomics and biomarker discovery[11], nucleic acid therapeutics[12], drug delivery[13] and controlled release systems[14], molecular engineering[15], and biosensors.

The selection processes giving rise to aptamers were developed independently in 1990 by the Gold and Szostak labs[16]. Commercial ventures based on aptamer technology have emerged, including Macugen (pegaptanib), an FDA-approved drug for wet AMD[17], and the clinical diagnostic company SomaLogic[18]. The International Society on Aptamers (INSOAP), a professional society for the aptamer research community, publishes an official journal devoted to the topic, Aptamers. While many aptamer databases are no longer online[19], Apta-index is a current database cataloging over 700 aptamers against a wide range of targets.

Etymology

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."[20]. Aptamers are occasionally referred to as "chemical antibodies" or "antibody mimics"[21].

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.[22]

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.[23] In the ensuing decades, directed evlution was used to develop new functions in a range of bacterial proteins[24][25]. In addition, a year before the publishing of in vitro selection and SELEX, Gerald Joyce used directed evolution to alter the cleavage activity of a ribozyme[26].

In 1990, two labs independently developed the technique of selection: the Gold lab, using the term SELEX for their process of selecting RNA ligands against T4 DNA polymerase[27]; and the Szostak lab, selecting RNA ligands against various organic dyes[28][29]. Two years later, the Szostak lab and Gilead Sciences, independent of one another, used in vitro selection schemes to evolve single stranded DNA ligands for organic dyes and human coagulant, thrombin (see anti-thrombin aptamers), respectively.

Since the discovery of aptamers, many researchers have used aptamer selection as a means for application and discovery. In 2001, the process of in vitro selection was automated[30][31][32] by J. Colin Cox in the Ellington lab at the University of Texas at Austin, reducing the duration of a selection experiment from six weeks to three days.

While the process of artificial engineering of nucleic acid ligands is highly interesting to biology and biotechnology, the notion of aptamers in the natural world had yet to be uncovered until 2002 when two groups led by Ronald Breaker and Evgeny Nudler discovered a nucleic acid-based genetic regulatory element (which was named riboswitch) that possesses similar molecular recognition properties to the artificially made aptamers. In addition to the discovery of a new mode of genetic regulation, this adds further credence to the notion of an 'RNA World', a postulated stage in time in the origins of life on Earth.

Properties

Structure

Most aptamers are based on a specific oligomer sequence, typically 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[33][34][35][36]. 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 have much greater potential combinatorial diversity per unit length. Chemical modifications of nucleic acid bases or backbones increase the chemical diversity of standard nucleic acid bases.

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. Unmodified aptamer applications currently focus on treating transient conditions such as blood clotting, or treating organs such as the eye where local delivery is possible. This rapid clearance can be an advantage in applications such as in vivo diagnostic imaging. Several modifications, such as 2'-fluorine-substituted pyrimidines and polyethylene glycol (PEG) linkage, permit a serum half-life of days to weeks.

Split aptamers are composed of two or more DNA strands that mimic segments of a larger parent aptamer[37]. The ability of each component strand to bind targets will depend on the location of the nick and the secondary structures of the daughter strands, with the most prominent structures being three-way junctions.[38] The presence of a target molecule can promote assembly of the DNA fragments, providing a potential template for biosensors in analogy to split protein systems[39]. Once assembled, the strands can be chemically or enzymatically ligated into a single strand. Analytes for which split aptamers have been developed include the protein α-thrombin, ATP, and cocaine.

Targets

Aptamer targets can include small molecules and heavy metal ions, larger ligands such as proteins, and even whole cells.[40][41]. These targets include lysozyme,[42] thrombin,[43] human immunodeficiency virus trans-acting responsive element (HIV TAR),[44] hemin,[45] interferon γ,[46] vascular endothelial growth factor (VEGF),[47] prostate specific antigen (PSA),[48][49] dopamine,[50] and the non-classical oncogene, heat shock factor 1 (HSF1).[51] In the case of lysozyme, HIV TAR, VEGF and dopamine the DNA aptamer is the analog of the RNA aptamer, with thymine replacing uracil. The hemin, thrombin, and interferon γ DNA and RNA aptamers were selected through independent selections and have unique sequences.

At the molecular level, the aptamer-ligand interaction is mediated through non-covalent forces, including electrostatic interactions, hydrophobic interactions, pi stacking, and hydrogen bonding.

Peptide Aptamers

Structure

While most aptamers are based on nucleic acids, peptide aptamers [52] 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.[53] 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,[54] 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

Peptide aptamer selection can be made using different systems, but the most used is currently 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 biopannings. Among peptides obtained from biopannings, mimotopes can be considered as a kind of peptide aptamers. All the peptides panned from combinatorial peptide libraries have been stored in a special database with the name MimoDB.[55][56]

Selection of Ligand Regulated Peptide Aptamers (LiRPAs) has been demonstrated. By displaying 7 amino acid peptides from a novel scaffold protein based on the trimeric FKBP-rapamycin-FRB structure, interaction between the randomized peptide and target molecule can be controlled by the small molecule Rapamycin or non-immunosuppressive analogs.

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.[57][58] 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.[59]

Applications

Aptamers can be used as:

Aptamers have also been generated against bacteria[74] and viruses including influenza A and B viruses,[75] Respiratory syncytial virus (RSV),[75] SARS coronavirus (SARS-CoV)[75] and SARS-CoV-2[76].

Antibody replacement

Aptamers can replace antibodies in many biotechnology applications[77][78]. In laboratory research and clinical diagnostics, they can be used in aptamer-based versions of immunoassays including ELISA[79], western blot[80], IHC[81], and flow cytometry[82]. As therapeutics, they can function as agonists or antagonists of their ligand[83]. 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[84]. Unlike antibodies, unmodified aptamers are more susceptible to nuclease digestion in serum and renal clearance in vivo. When aptamers are available for a particular application, their potentially lower immunogenicity, greater replicability and lower cost, flexibility of development against novel targets and environments, and capacity to be engineered for enhanced durability, specificity, and sensitivity make them potentially attractive alternatives to antibodies[85]. In addition, aptamers contribute to reduction of research animal use[86]. While antibodies 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.

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 affinity strength to passively release the growth factors,[87] along with active release via mechanisms such as hybridization of the aptamer with complementary oligonucleotides[88] or unfolding of the aptamer due to cellular traction forces.[89]

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.[90]

AptaBiD

AptaBiD or Aptamer-Facilitated Biomarker Discovery is a technology for biomarker discovery.[91] AptaBiD is based on multi-round generation of an aptamer or a pool of aptamers for differential molecular targets on the cells which facilitates exponential detection of biomarkers. It involves three major stages: (i) differential multi-round selection of aptamers for biomarker of target cells; (ii) aptamer-based isolation of biomarkers from target cells; and (iii) mass spectrometry identification of biomarkers. The important feature of the AptaBiD technology is that it produces synthetic affinity probes (aptamers) simultaneously with biomarker discovery. In AptaBiD, aptamers are developed for cell surface biomarkers in their native state and conformation. In addition to facilitating biomarker identification, such aptamers can be directly used for cell isolation, cell visualization, and tracking cells in vivo. They can also be used to modulate activities of cell receptors and deliver different agents (e.g., siRNA and drugs) into the cells.

See also

References

  1. ^ 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. doi:10.1016/j.bios.2016.04.091.
  2. ^ Nudler, Evgeny; Mironov, Alexander (2004). "The riboswitch control of bacterial metabolism". Trends in biochemical sciences. doi:10.1016/j.tibs.2003.11.004.
  3. ^ Gopinath, Subash (2007). "Methods developed for SELEX". Analytical and Bioanalytical Chemistry. doi:10.1007/s00216-006-0826-2.
  4. ^ Gao, Shunxiang (2016). "Post-SELEX optimization of aptamers". Analytical and bioanalytical chemistry. doi:10.1007/s00216-016-9556-2.
  5. ^ Kalra, Priya (2018). "Simple methods and rational design for enhancing aptamer sensitivity and specificity". Frontiers in molecular biosciences. doi:10.3389/fmolb.2018.00041.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  6. ^ Berezovski, Maxim (2006). "Non-SELEX selection of aptamers". Journal of the American Chemical Society.
  7. ^ Wang, R.E. (2011). "Improving the Stability of Aptamers by Chemical Modification". Current Medicinal Chemistry. doi:10.2174/092986711797189565.
  8. ^ Feagin, Trevor; Maganzini, Nicolò; Soh, Hyongsok. "Strategies for Creating Structure-Switching Aptamers". ACS sensors. doi:10.1021/acssensors.8b00516.
  9. ^ Song, Shiping (2008). "Aptamer-based biosensors". TrAC Trends in Analytical Chemistry.
  10. ^ Tombelli, Sara; Minunni, Maria; Mascini, Marco (2007). "Aptamers-based assays for diagnostics, environmental and food analysis". Biomolecular engineering. doi:10.1016/j.bioeng.2007.03.003.
  11. ^ Huang, Jie (2021). "Advances in aptamer-based biomarker discovery". Frontiers in Cell and Developmental Biology. doi:10.3389/fcell.2021.659760.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  12. ^ Keefe, Anthony; Pai, Supriya; Ellington, Andrew. "Aptamers as therapeutics". doi:10.1038/nrd3141. {{cite journal}}: Cite journal requires |journal= (help)
  13. ^ Jiehua, Zhou; Rossi, John (2011). "Cell-specific aptamer-mediated targeted drug delivery". Oligonucleotides. doi:10.1089/oli.2010.0264.
  14. ^ Farokhzad, Omid; Karp, Jeffrey; Langer, Robert (2006). "Nanoparticle-aptamer bioconjugates for cancer targeting". Expert opinion on drug delivery. doi:10.1517/17425247.3.3.311.
  15. ^ Lin, Yun; Jayasena, Sumedha (1997). "Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer". Journal of molecular biology. doi:10.1006/jmbi.1997.1165.
  16. ^ Gold, Larry (2015). "SELEX: How it happened and where it will go". Journal of Molecular Evolution. doi:10.1007/s00239-015-9705-9.
  17. ^ "FDA Approves Eyetech/Pfizer's Macugen". Review of Opthamology. Retrieved 30 June 2022.
  18. ^ Dutt, Sreetama. "SomaLogic and Illumina Combine Strengths to Propel Innovation in Proteomics". BioSpace. Retrieved 30 June 2022.
  19. ^ Darmostuk, Maria (2015). "Current approaches in SELEX: An update to aptamer selection technology". Biotechnology advances.
  20. ^ Ellington, Andrew; Szostak, Jack (1990). "In vitro selection of RNA molecules that bind specific ligands". Nature. doi:10.1038/346818a0.
  21. ^ Gang, Zhou (2016). "Aptamers: A promising chemical antibody for cancer therapy". Oncotarget. doi:10.18632/oncotarget.7178.
  22. ^ Joyce, Gerald (1994). "In vitro evolution of nucleic acids". Current opinion in structural biology. doi:10.1016/S0959-440X(94)90100-7.
  23. ^ 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.
  24. ^ 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.
  25. ^ Hall, Barry (1981). "Changes in the substrate specificities of an enzyme during directed evolution of new functions". Biochemistry.
  26. ^ Joyce, Gerald (1989). "Amplification, mutation and selection of catalytic RNA". Gene.
  27. ^ Tuerk, Craig; Gold, Larry (1990). "Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase". Science.
  28. ^ Ellington, Andrew; Szostak, Jack (1990). "In vitro selection of RNA molecules that bind specific ligands". Nature.
  29. ^ Stoltenburg, Regina; Strehlitz, Beate (2007). "SELEX—a (r) evolutionary method to generate high-affinity nucleic acid ligands". Biomolecular engineering.
  30. ^ 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.
  31. ^ 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.
  32. ^ 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.
  33. ^ 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.
  34. ^ 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.
  35. ^ 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.
  36. ^ 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.
  37. ^ Chen, Ailiang; Yan, Mengmeng; Yang, Shuming (2016). "Split aptamers and their applications in sandwich aptasensors". TrAC Trends in Analytical Chemistry.
  38. ^ 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.
  39. ^ 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.
  40. ^ 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.
  41. ^ 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.
  42. ^ 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.
  43. ^ 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.
  44. ^ 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.
  45. ^ 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.
  46. ^ 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.
  47. ^ 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.
  48. ^ 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.
  49. ^ 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.
  50. ^ 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.
  51. ^ 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.
  52. ^ 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.
  53. ^ Nolan GP (January 2005). "Tadpoles by the tail". Nature Methods. 2 (1): 11–12. doi:10.1038/nmeth0105-11. PMID 15782163. S2CID 1423778.
  54. ^ 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.
  55. ^ 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.
  56. ^ "MimoDB: a mimotope database and beyond". immunet.cn. Archived from the original on 2012-11-16. Retrieved 2016-02-03.
  57. ^ 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.
  58. ^ 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)
  59. ^ 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.
  60. ^ 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.
  61. ^ 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.
  62. ^ 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.
  63. ^ 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.
  64. ^ 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.
  65. ^ 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.
  66. ^ Penner, Gregory (July 2012). "Commercialization of an aptamer-based diagnostic test" (PDF). NeoVentures.
  67. ^ 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.
  68. ^ 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.
  69. ^ 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.
  70. ^ 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.
  71. ^ 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)
  72. ^ 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.
  73. ^ 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.
  74. ^ 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.
  75. ^ 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.
  76. ^ 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.
  77. ^ Chen, Ailiang; Yang, Shuming (2015). "Replacing antibodies with aptamers in lateral flow immunoassay". Biosensors and bioelectronics.
  78. ^ Bauer, Michelle (2019). "Anything you can do, I can do better: Can aptamers replace antibodies in clinical diagnostic applications?". Molecules.
  79. ^ Toh, Saw Yi (2015). "Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay". Biosensors and bioelectronics. doi:10.1016/j.bios.2014.09.026.
  80. ^ 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.
  81. ^ Bauer, Michelle (2016). "The application of aptamers for immunohistochemistry". Nucleic acid therapeutics. doi:10.1089/nat.2015.0569.
  82. ^ Meyer, Michael; Scheper, Thomas; Walter, Johanna-Gabriela (2013). "Aptamers: versatile probes for flow cytometry". Applied microbiology and biotechnology.
  83. ^ Zhou, Jiehua; Rossi, John (2017). "Aptamers as targeted therapeutics: current potential and challenges". Nature reviews Drug discovery.
  84. ^ Bruno, John (2015). "Predicting the Uncertain Future of Aptamer-Based Diagnostics and Therapeutics". Molecules.
  85. ^ Wang, Tao (2019). "Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development". Biotechnology advances.
  86. ^ Melbourne, Jodie (2016). "A Multi-faceted Approach to Achieving the Global Acceptance of Animal-free Research Methods". Alternatives to Laboratory Animals.
  87. ^ 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.
  88. ^ 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.
  89. ^ 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.
  90. ^ Sahara Hot Start PCR Master Mix
  91. ^ 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.

Further reading

Retrieved from "https://en.wikipedia.org/w/index.php?title=Aptamer&oldid=1095864271"