The electromechanics of DNA in a synthetic nanopore

Biophysical Journal

Volumn 90, Issue 3, 2006, Pages 1098-1106

  Heng, J B ^a   Aksimentiev, A ^a   Ho, C ^a   Marks, P ^a   Grinkova, Y V ^b   Sligar, S ^b   Schulten, K ^a   Timp, G ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED DNA; SILICON NITRIDE; SINGLE STRANDED DNA;

ALKALINITY; ARTICLE; ARTIFICIAL MEMBRANE; DNA HELIX; ELECTRIC FIELD; ELECTROCHEMISTRY; MEMBRANE PERMEABILITY; MOLECULAR DYNAMICS; NANOTECHNOLOGY; POROSITY; SYNTHESIS;

EID: 33645542434     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.070672     Document Type: Article

References (32)

1. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer-Verlag, New York.
2. Kasianowicz, J. J., E. Brandin, D. Branton, and D. W. Deamer. 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA. 93:13770-13773.
3. Bayley, H., and P. S. Cremer. 2001. Stochastic sensors inspired by biology. Nature. 413:226-230.
4. Heng, J. B., C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. 2004. Sizing DNA using a nanometer-diameter pore. Biophys. J. 87:2905-2911.
5. Akeson, M., D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer. 1999. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77:3227-3233.
6. Heng, J. B., A. Aksimentiev, C. Ho, V. Dimitrov, T. Sorsch, J. Miner, W. Mansfield, K. Schulten, and G. Timp. 2005. Beyond the gene chip. Bell Labs Technical Journal. 10:5-22.
7. Chang, H., F. Kosari, G. Andreadakis, M. A. Alam, G. Vasmatzis, and R. Bashir. 2004. DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels. Nano Lett. 4:1551-1556.
8. Henrickson, S. E., M. Misakian, B. Robertson, and J. J. Kasianowicz. 2000. Driven DNA transport into an asymmetric nanometer-scale pore. Phys. Rev. Lett. 85:3057-3060.
9. Li, J., M. Gershow, D. Stein, E. Brandin, and J. A. Golovchenko. 2003. DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2:611-615.
10. Storm, A. J., J. H. Chen, H. W. Zandbergen, and C. Dekker. 2005. Translocation of double-strand DNA through a silicon oxide nanopore. Phys. Rev. E. 71:051903-051912.
11. Ambjörnsson, T., S. P. Apell, Z. Konkoli, E. A. DiMarzio, and J. J. Kasianowicz. 2002. Charged polymer membrane translocation. J. Chem. Phys. 117:4063-4073.
12. Bustamante, C., S. B. Smith, J. Liphardt, and D. Smith. 2000. Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol. 10:279-285.
13. Cluzel-Schaumann, H., M. Rief, C. Tolksdorf, and H. E. Gaub. 2000. Mechanical stability of single DNA molecules. Biophys. J. 78:1997-2007.
14. Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
15. Heng, J. B., A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. 2005. Stretching DNA using the electric field in a synthetic nanopore. Nano Lett. 5:1883-1888.
16. Ho, C., R. Qiao, J. B. Heng, A. Chatterjee, R. Timp, N. R. Aluru, and G. Timp. 2005. Electrolytic transport through a synthetic nanometer-diameter pore. Proc. Natl. Acad. Sci. USA. 102:10445-10450.
17. Aksimentiev, A., J. B. Heng, G. Timp, and K. Schulten. 2004. Microscopic kinetics of DNA translocation through synthetic nanopores. Biophys. J. 87:2086-2097.
18. Polygen. 1988. Quanta Polygen Corporation, Waltham, MA.
19. Kalé, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
20. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
21. 4. J. Chem. Phys. 97:5048-5062.
22. Xu, D., J. C. Phillips, and K. Schulten. 1996. Protein response to external electric fields: relaxation, hysteresis and echo. J. Phys. Chem. 100:12108-12121.
23. Schmidt, M. W., K. K. Baldridge, J. A. Boatz, S. Elbert, M. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. Shujun, T. Windus, M. Dupuis, and J. A. Montgomery. 1993. General atomic and molecular electronic structure system. J. Comput. Chem. 14:1347-1363.
24. Bayly, C. I., P. Cieplak, W. D. Cornell, and P. A. Kollman. 1993. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97:10269-10280.
25. Szabò, I., G. Bàthori, F. Tombola, A. Coppola, I. Schmehl, M. Brini, A. Ghazi, V. De Pinto, and M. Zoratti. 1998. Double-stranded DNA can be translocated across a planar bilayer containing purified mitochondrial porin. FASEB J. 12:495-502.
26. Storm, A. J., C. Storm, J. Chen, H. Zandbergen, J.-F. Joanny, and C. Dekker. 2005. Fast DNA translocation through a solid-state nanopore. Nano Lett. 5:1193-1197.
27. Mathe, J., A. Aksimentiev, D. R. Nelson, K. Schulten, and A. Meller. 2005. Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel. Proc. Natl. Acad. Sci. USA. 102:12377-12382.
28. Meller, A., L. Nivon, and D. Branton. 2001. Voltage-driven DNA translocations through a nanopore. Phys. Rev. Lett. 86:3435-3438.
29. Yeh, I. C., and G. Hummer. 2004. Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 101:12177-12182.
30. Harris, S. A., Z. A. Sands, and C. A. Laughton. 2005. Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys. J. 88:1684-1691.
31. Williams, M. C., J. R. Wenner, I. Rouzina, and V. A. Bloomfield. 2001. The effect of pH on the overstretching transition of dsDNA: evidence of force-induced DNA melting. Biophys. J. 80:874-881.
32. Rouzina, I., and V. A. Bloomfield. 2001. Force-induced melting of the DNA double helix. II. Effect of solution conditions. Biophys. J. 80:894-900.