Journal of Advances in Nanomaterials
DNA Nanodevices Confined on DNA Origamis: an Isothermal Ratchet Driven by Boundary Conditions
Download PDF (839.1 KB) PP. 208 - 218 Pub. Date: December 7, 2017
Author(s)
- Jean-Pierre Aime*
VIBBnano,CBMN Ave Geoffroy St Hilaire CNRS University Bordeaux Pessac 33600, France - Juan Elezgaray
VIBBnano,CBMN Ave Geoffroy St Hilaire CNRS University Bordeaux Pessac 33600, France - Oscar Mendoza
VIBBnano,CBMN Ave Geoffroy St Hilaire CNRS University Bordeaux Pessac 33600, France
Abstract
Keywords
References
[1] N. C. Seeman. Nucleic acid junctions and lattices. J. Theor. Biol., 99:237–247, 1982.
[2] N. C. Seeman. Nanomaterials based on dna. Annu. Rev. Biochem., 79:65–87, 2010.
[3] P. Rothemund. Folding dna to create nanoscale shapes and patterns. Nature, 440:297–302, 2006.
[4] B. Yurke, A. Tuberfield, Allen P. Mills, F.C. Simmel, and J.L. Neumann. A dna-fuelled molecular machine made of dna. Nature, 406:605–608, 2000.
[5] D. Soloveichik. Dna as a universal substrate for chemical kinetics. Proc. Natl Acad. Sci. USA, 107:5393–5398, 2010.
[6] A. J. Turberfield, J. C. Mitchell, B. Yurke, A. P. Mills, M. I. Blakey, and F. C. Simmel. Dna fuel for free-running nanomachines. Phys. Rev. Lett., 90:118102, 2003.
[7] F. C. Simmel and B. Yurke. A dna-based molecular device switchable between three distinct mechanical states. Appl. Phys. Lett., 80:883–885, 2002.
[8] B. Yurke. Using dna to power nanostructures. Genet. Program. Evolvable Machines, 4:111–122, 2003.
[9] L. Qian and E. Winfree. Scaling up digital circuit computation with dna strand dis-placement cascades. Science, 332:1196–1201, 2011.
[10] B. Li, A. D. Ellington, and X. Chen. Rational, modular adaptation of enzyme-free dna circuits to multiple detection methods. Nucleic Acids Research, 39:No. 16, e110, 2011.
[11] K. Montagne, R. Plasson, Y. Sakai, T. Fujii, and Y. Rondelez. Programming an in vitro dna oscillator using a molecular networking strategy. Molecular Systems Biology, 7:Article number 466, 2011.
[12] P. Alberti and J.L. Mergny. Dna duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc. Natl. Acad. Sci., 100:1569–1573, 2003.
[13] K. Lund, A. J. Manzo, N. Dabby, N. Michelotti, A. Johnson-Buck, J. Nangreave, S.Taylor, R. Pei, M. N. Stojanovic, N. G. Walter, E. Winfree, and H. Yan. Molecular robots guided by prescriptive landscapes. Nature, 465:206–210, 2010.
[14] J. S. Shin and N.A. Pierce. A synthetic dna walker for molecular transport. J. Am. Chem. Soc., 126:10834– 10835, 2004.
[15] P. Yin, H. Yan, A. J. Turberfield X. G. Daniell, and J.H. Reif. A unidirectional dna walker that moves autonomously along a track. Angew. Chem. Int. Ed., 43:4906–4911, 2004.
[16] S. F. J. Wickham, J. Bath, Y. Katsuda, M. E. K. Hidaka, H. Sugiyama, and A.J. Turberfield. A dna-based molecular motor that can navigate a network of tracks. Nature Nanotechnology, 7:169–173, 2012.
[17] T. Omabegho, R. Sha, and N. C. Seeman. A bipedal dna brownian motor with coordinated legs. Science, 324:67–71, 2009.
[18] S.M. Douglas, I. Bachelet, and G.M. Church. A logic-gated nanorobot for targeted transport of molecular payloads. Science, 335:831–834, 2012.
[19] E. S. Andersen, M. Dong, M. M. Nielsen, K. Jahn, R. Subramani, W. Mamdouh, M. M. Golas, B. Sander, H. Stark, C. L. P. Oliveira, V. Petersen, J. S. ;and Birkedal, F. Besenbacher, K. V. Gothelf, and J. Kjems. Self-assembly of a nanoscale dna box with a controllable lid. Nature, 459:73–76, 2009.
[20] Uri Alon. An introduction to systems biology. Chapman and Hall/CRC press, Taylor and Francis, 2007.
[21] William Bialek. Biophysics. searching for principles. Princeton University Press, 2012.
[22] Eric R. Kandel, James H. Schwartz, and Thomas M. Jessel. Principles of neural science. McGraw-Hill, Fourth Edition, 2000.
[23] Ismael Mullor Ruiz, Jean-Michel Arbona, Amitkumar Lad, Oscar Mendoza, Jean-Pierre Aimé, and Juan Elezgaray. Connecting localized dna strand displacement reactions. Nanoscale, 7:12970, 2015.
[24] D. Y. Zhang and E. Winfree. Control of dna strand displacement kinetics using toehold exchange. J. Am. Chem. Soc., 131:17303–17314, 2009.
[25] D.Y. Zhang. Dynamic dna strand displacement circuits. Thesis, California Institute of Technology Pasadena, California., May 2010.
[26] D.Y. Zhang and G. Seelig. Dynamic dna nanotechnology using strand-displacement reactions. Nat. Chem., 3:103–113, 2011.
[27] Jean-Pierre Aimé and Juan Elezgaray. Dna nano devices as a biased random walk process: A case study of isothermal ratchet? Materials Sciences and Applications, 6:401–419, 2015.
[28] S. Alexander and P. Pincus. Diffusion of labeled particles on one-dimensional chains. Physical Review B, 18(4):2011–2012, 1978.
[29] P Sekhar Burada, Peter H?nggi, Fabio Marchesoni, Gerhard Schmid, and Peter Talkner. Diffusion in confined geometries. ChemPhysChem, 10(1):45–54, 2009.
[30] Oscar Mendoza, Jean-Pierre Aimé, and Juan Elezgaray. Dna computing using strand displacement: Localized amplification circuits (lac) dna origami and diluted solution. submitted, 2016.
[31] E. Ben-Naim and P.L. Krapivsky. Enhanced diffusion in disordered systems. Phys. Rev. Lett., 102:190602, 2009.
[32] Jean-Philippe Bouchaud and Antoine Georges. Anomalous diffusion in disordered media: Statistical mehcanism, models and physical applications. PHYSICS REPORTS, 195:127–293, 1990.
[33] Byung Mook Weon and Jung Ho Je. Theoretical estimation of maximum human lifespan. Biogerontology, 10:65–71, 2009.
[34] Masaki Sasai Hironori K. Nakamura and Mitsunori Takano. Scrutinizing the squeezed exponential kinetics observed in the folding simulation of an off-lattice go-like protein model. Chemical Physics, 307:259–267, 2004.
[35] Oscar Mendoza, Jean-Louis Mergny, Jean-Pierre Aimé, and Juan Elezgaray. G quadruplexes light up localized dna circuits. Nano Letters, 16:624, 2016.
[36] N. Srinivas, T. E. Ouldridge, P. Sulc, J.M. Schaeffer, B. Yurke, A.A. Louis, J. P. K. Doye, and E. Winfree. On the biophysics and kinetics of toehold-mediated dna strand displacement. Nucleic Acids Research, 41:10641–10658, 2013.