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DNA walker

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This is an old revision of this page, as edited by Johnreif (talk | contribs) at 23:21, 20 June 2020 (combined two citations of same Shin paper, and defined nonautonomous and nonautonomous DNA walkers). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

A DNA walker is a class of nucleic acid nanomachines where a nucleic acid "walker" is able to move along a nucleic acid "track". The concept of a DNA walker was first defined and named by John H. Reif in 2003.[1] A nonautonomous DNA walker requires external changes for each step, whereas an autonomous DNA walker progresses without any external changes. Various nonautonomous DNA walkers were developed, for example Shin [2] controlled the motion of DNA walker by using 'control strands' which needed to be manually added in a specific order according to the template's sequence in order to get the desired path of motion. In 2004 the first autonomous DNA walker, which did not require external changes for each step, was experimentally demonstrated by the Reif group. [3]

DNA walkers have functional properties such as a range of motion extending from linear to 2 and 3-dimensional, the ability to pick up and drop off molecular cargo,[4] performing DNA-templated synthesis, and increased velocity of motion. DNA walkers have potential applications ranging from nanomedicine to nanorobotics.[5][6][7] Many different fuel options have been studied including DNA hybridization, hydrolysis of DNA or ATP, and light.[8] The DNA walker's function is similar to that of the proteins dynein and kinesin.[5]

Role in DNA nanotechnology

Finding a suitable nanoscale motor capable of autonomous, unidirectional, linear motion is considered important to the development of DNA nanotechnology.[5][6] The walkers have been shown to be capable of autonomous motion over linear, 2-dimensional and 3-dimensional DNA 'tracks' through a large number of schemes. In July 2005, Bath et al. showed that another way to control DNA walker motion is to use restriction enzymes to strategically cleave the 'track', causing the forward motion of the walkers.[9] In 2010, two different sets of researchers exhibited the walkers' more complex abilities to selectively pick up and drop off molecular cargo[10][11] and to perform DNA-templated synthesis as the walker moves along the track.[12] In late 2015, Yehl et al. showed that three orders of magnitude higher than the speeds of motion seen previously were possible when using DNA-coated spherical particles that would "roll" on a surface modified with RNA complementary to the nanoparticle's DNA. RNase H was used to hydrolyse the RNA, releasing the bound DNA and allowing the DNA to hybridize to RNA further downstream.[13]

Applications

The applications of DNA walkers include nanomedicine,[14] diagnostic sensing of biological samples,[15] nanorobotics[16] and much more.[7] In late 2015, Yehl et al. improved the DNA walker's function by increasing its velocity, and it has been proposed as the basis for a low-cost, low-tech diagnostics machine capable of detecting single nucleotide mutations and heavy-metal contamination in water.[15]. In 2018 Nils Walter and his team designed a DNA walker that is capable of moving at a speed of 300 nanometres per minute. This is an order of magnitude faster than the pace of other types of DNA walker.[17]

See also

References

  1. ^ Reif, John H. (2003). "The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA". Natural Computing. 2 (15): 439–461. CiteSeerX 10.1.1.4.291. doi:10.1023/B:NACO.0000006775.03534.92.
  2. ^ Shin, Jong-Shik (8 September 2004). "A synthetic DNA walker for molecular transport" (PDF). Journal of the American Chemical Society. 126 (35): 10834–5. doi:10.1021/ja047543j. PMID 15339155.
  3. ^ Yin, Peng; Yan, Hao; Daniel, Xiaoju G.; Turberfield, Andrew J.; Reif, John H. (2004). "A Unidirectional DNA Walker Moving Autonomously Along a Linear Track". Angewandte Chemie International Edition. 43 (37): 4906–4911. doi:10.1002/anie.200460522. PMID 15372637.
  4. ^ Thubagere, Anupama J.; Li, Wei; Johnson, Robert F.; Chen, Zibo; Doroudi, Shayan; Lee, Yae Lim; Izatt, Gregory; Wittman, Sarah; Srinivas, Niranjan (2017-09-15). "A cargo-sorting DNA robot". Science. 357 (6356): eaan6558. doi:10.1126/science.aan6558. ISSN 0036-8075. PMID 28912216.
  5. ^ a b c Simmel, Friedrich (September 8, 2009). "Processive Motion of Bipedal DNA Walkers". ChemPhysChem. 10 (15): 2593–7. doi:10.1002/cphc.200900493. PMID 19739195.
  6. ^ a b Pan, Jing (August 2015). "Recent progress on DNA based walkers". Curr Opin Biotechnol. 34: 56–64. doi:10.1016/j.copbio.2014.11.017. PMID 25498478.
  7. ^ a b Leigh, David (April 2014). Synthetic DNA Walkers. Topics in Current Chemistry. Vol. 354. pp. 111–38. doi:10.1007/128_2014_546. ISBN 978-3-319-08677-4. PMID 24770565. {{cite book}}: |journal= ignored (help)
  8. ^ You, Mingxu (Mar 5, 2012). "An Autonomous and Controllable Light-Driven DNA Walking Device". Angewandte Chemie. 51 (10): 2457–60. doi:10.1002/anie.201107733. PMC 3843772. PMID 22298502.
  9. ^ Bath, Jonathan (July 11, 2005). "A free-running DNA motor powered by a nicking enzyme". Angewandte Chemie International Edition. 117 (28): 4432–4435. doi:10.1002/ange.200501262.
  10. ^ Lund, Kyle (May 13, 2010). "Molecular Robots Guided by Prescriptive Landscapes". Nature. 465 (7295): 206–10. Bibcode:2010Natur.465..206L. doi:10.1038/nature09012. PMC 2907518. PMID 20463735.
  11. ^ Gu, Hongzhou; Chao, Jie; Xiao, Shou-Jun; Seeman, Nadrian C. (2010). "A proximity-based programmable DNA nanoscale assembly line". Nature. 465 (7295): 202–205. Bibcode:2010Natur.465..202G. doi:10.1038/nature09026. PMC 2872101. PMID 20463734.
  12. ^ He, Yu (Nov 5, 2010). "Autonomous Multistep Organic Synthesis in a Single Isothermal Solution Mediated by a DNA Walker". Nat Nanotechnol. 5 (11): 778–82. Bibcode:2010NatNa...5..778H. doi:10.1038/nnano.2010.190. PMC 2974042. PMID 20935654.
  13. ^ Yehl, Kevin (Nov 30, 2015). "High-speed DNA-based rolling motors powered by RNase H". Nature Nanotechnology. 11 (2): 184–90. Bibcode:2016NatNa..11..184Y. doi:10.1038/nnano.2015.259. PMC 4890967. PMID 26619152.
  14. ^ Boehm, Frank (Nov 18, 2013). Nanomedical Device and Systems Design: Challenges, Possibilities, Visions. CRC Press. ISBN 9781439863237.
  15. ^ a b "Nano-walkers take speedy leap forward with first rolling DNA-based motor". phys.org. Phys.org. Retrieved 2015-12-04.
  16. ^ "Chapter 18 : DNA Nano Robotics – NanoTechnology Journal & Publications". NanoTechnology Journal & Publications. Archived from the original on 2015-12-08. Retrieved 2015-12-04.
  17. ^ "Gymnastic feats help DNA 'walker' set speed record". Nature. 557 (7705): 283. 2018. doi:10.1038/d41586-018-05127-8. PMID 29760489.
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