Can an atomic force microscope sequence DNA using a nanopore?

Biophysical Journal

Volumn 94, Issue 4, 2008, Pages 1233-1240

  Qamar, Shahid ^a   Williams, Phil M ^b   Lindsay, S M ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NANOMATERIAL;

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DNA SEQUENCE; ELASTICITY; MECHANICAL STRESS; METHODOLOGY; ULTRASTRUCTURE;

COMPUTER SIMULATION; DNA; ELASTICITY; MICROSCOPY, ATOMIC FORCE; MODELS, CHEMICAL; MODELS, MOLECULAR; NANOSTRUCTURES; NUCLEIC ACID CONFORMATION; SEQUENCE ANALYSIS, DNA; STRESS, MECHANICAL;

EID: 38949206625     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.108670     Document Type: Article

References (35)

1. Astier, Y., O. Braha, and H. Bayley. 2006. Toward single molecule DNA sequencing: Direct identification of ribonucleoside and deoxy-ribonucleoside 5′ monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J. Am. Chem. Soc. 128: 1705-1710.
2. Mathe, J., A. Arinstein, Y. Rabin, and A. Meller. 2006. Equilibrium and irreversible unzipping of DNA in a nanopore. Europhys. Lett. 73: 128-134.
3. Heng, J., A. Aksimentiev, C. Ho, and P. Marks. 2006. The electromechanics of DNA in a synthetic nanopore. Biophys. J. 90: 1098-1106.
4. Heng, J., V. Dimitrov, Y. Grinkova, and C. Ho. 2003. The detection of DNA using a silicon nanopore. Presented in Electron Devices Meeting, IEDM 2003 Technical Digest. IEEE International.
5. Meller, A. 2000. Rapid nanopore discrimination between single poly- nucleotide molecules. Proc. Natl. Acad. Sci. USA. 97:1079-84.
6. Sanger, F., S. Nicklen, and A. Coulson. 1977. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA. 74:5463-7.
7. Kasianowicz, J. J., E. Brandin, D. Branton, and D. W. Deamer. 1996. Characterization of individual polynucleotide molecules using membrane channel. Proc. Natl. Acad. Sci. USA. 93:13770-3.
8. Fologea, D. 2005. Detecting single stranded DNA with a solid state nanopore. Nano Lett. 5:1905-1909.
9. Akeson, M., D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer. 1999. Microsecond time scale discrimination among poly- cytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77:3227-33.
10. Spadola, Q., S. Qamar, B. Ashcraft, P. Zhang, and S. M. Lindsay. 2006. Assembly of DNA Rotaxane for AFM Based DNA Sequencing. Cellular Structure and Molecular Dynamic. Nanotech 2006 Proc.Boston.
11. Hiroshi, O. 1983. Syntheses and properties of rotaxane complex. Inorg. Chem. 23:3312-3316.
12. Bension, R. 2004. Rapid sequencing of polymers. US patent application (2004 0214177).
13. Faradjian, A., and R. Elber. 2004. Computing time scales from reaction coordinates by milestoning. J. Chem. Phys. 120:10880-9.
14. Evans, E. 1998. Energy landscapes biomolecular adhesion and receptor anchoring at interface explored with dynamics force microscopy. Faraday Discuss. 111:1-16.
15. Qamar, S., B. Ashcraft, Q. Spadola, P. Williams, P. Zhang, and S. M. Lindsay. 2006. DNA Translocation through a Nanopore. Computational Modeling in Life Science. Nanotech 2006 Proc. 2:329-332.
16. Cornell, W. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
17. Foloppe, N., and A. MacKerell. 2000. All atoms empirical force field of nucleic acid. J. Comput. Chem. 21:86-104.
18. Kalé, L. 1999. Greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
19. Pearlman, D. 1995. A package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp (AMBER).
20. Jorgensen, W. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
21. Martyna, G. 1994. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101:4177-4189.
22. Berendsen, H. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
23. 23.Feller, S. 1995. Constant pressure molecular dynamics simulation: the Langevin piston method. 103:4613-4621.
24. Allen, M. 1987. Computer Simulations of Liquids. Oxford University Press, New York.
25. Ryckaert, J. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
26. Evans, E. 2001. Probing the relation between force-lifetime and chemistry in single molecular bonds. Annu. Rev. Biophys. Bioeng. 30:105-128.
27. Kramers, K. 1940. Model of diffusive barrier. Physica. 7:284.
28. Smith, S. B., Y. J. Cui, and C. Bustamante. 1996. Overstretching B-DNA the elastic response of individual double-stranded and single- stranded DNA molecules. Science. 271:795-9.
29. Karlin, S. 1975. A First Course in Stochastic Simulation, 2nd ed. New York.
30. Montroll, E. 1984. The Wonderful World of Random Walk Nonequi- librium Phenomena.
31. Gillespie, D. 1992. Markov Process. An Introduction for Physical Scientists. Academic Press, San Diego, CA.
32. Evans, E., K. Ritchie, and R. Markel. 1995. Sensitive force technique to probe molecular adhesion and structural linkage at biological interface. Biophys. J. 68:2580-2587.
33. Wells, S., S. Menor, B. Hespenheide, and M. F. Thorpe. 2005. Constrained geometric simulation of diffusive motion in proteins. Phys. Biol. 2:S127-S136.
34. Sartbaeva, A., S. A. Wells, and M. F. Thorpe. 2006. Geometric simulation of perovskite frameworks with Jahn-Teller distribution. Phys. Rev. Lett. 97:065501.
35. Hespenheide, B. M., D. J. Jacobs, and M. F. Thorpe. 2004. Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus. J. Phys. Condens. Matter. 16:S5055-S5064.