Microscopic kinetics of DNA translocation through synthetic nanopores

Biophysical Journal

Volumn 87, Issue 3, 2004, Pages 2086-2097

  Aksimentiev, Aleksij ^a   Heng, Jiunn B ^a   Timp, Gregory ^a   Schulten, Klaus ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

DNA BASE; DOUBLE STRANDED DNA; ELECTROLYTE; POTASSIUM CHLORIDE; SILICON NITRIDE; SINGLE STRANDED DNA; WATER;

ARTICLE; BASE PAIRING; DEVICE; DNA DETERMINATION; DNA SEQUENCE; ELECTRIC FIELD; ELECTROLYSIS; FEASIBILITY STUDY; HYDROPHOBICITY; ION CURRENT; KINETICS; MEMBRANE; MOLECULAR DYNAMICS; NANOTECHNOLOGY; SEMICONDUCTOR; SENSOR; SEQUENCE ANALYSIS; SIGNAL DETECTION; SIMULATION;

EID: 4444234147     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.042960     Document Type: Article

References (53)

1. Akenson, M., D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer. 1999. Microsecond timescale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77:3227-3233.
2. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Oxford University Press, New York.
3. Ambjörnsson, T., S. P. Apell, Z. Konkoli, E. A. D. Marzio, and J. J. Kasianowicz. 2002. Charged polymer membrane translocation. Biophys. J. 117:4063-4073.
4. Balaeff, A., C. R. Koudella, L. Mahadevan, and K. Schulten. 2004. Modeling DNA loops using continuum and statistical mechanics. Philos. Trans. R. Soc. Lond. A. In press.
5. Batcho, P. F., D. A. Case, and T. Schlick. 2001. Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. J. Chem. Phys. 115:4003-4018.
6. Beckstein, O., P. C. Biggin, and M. S. P. Sansom. 2001. A hydrophobic gating mechanism for nanopores. J. Phys. Chem. B. 105:12902-12905.
7. Beckstein, O., and M. S. P. Sansom. 2003. Liquid-vapor oscillations of water in hydrophobic nanopores. Proc. Natl. Acad. Sci. USA. 100:7063-7068.
8. + channel. Nature. 414:73-77.
9. Beveridge, D. L., and G. Ravishanker. 1994. Molecular dynamics studies of DNA. Curr. Opin. Struct. Biol. 4:246-255.
10. Brünger, A. T. 1992. X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
11. Chen, C.-M., and E.-H. Coalson. 2003. Nanopore sequencing of polynuclueotides assisted by a rotating electric field. Appl. Phys. Lett. 82:1308-1310.
12. Chern, S. S., A. E. Cárdenas, and R. D. Coalson. 2001. Three-dimensional dynamic Monte Carlo simulations of driven polymer transport through a hole in a wall. J. Chem. Phys. 115:7772-7782.
13. Chuang, J., Y. Kantor, and M. Kardar. 2001. Anomalous dynamics of translocation. Phys. Rev. E. Stat. Nonlin. Soft Matter. 65:011802.
14. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, J. 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.
15. Crozier, P. S., D. Henderson, R. L. Rowley, and D. D. Busath. 2001. Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics. Biophys. J. 81:3077-3089.
16. de Groot, B. L., and H. Grubmüller. 2001. Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science. 294:2353-2357.
17. 4. Acta Crystallogr. B35:800-804.
18. Gullingsrud, J., D. Kosztin, and K. Schulten. 2001. Structural determinants of MscL gating studied by molecular dynamics simulations. Biophys. J. 80:2074-2081.
19. Heng, J. B., V. Dimitrov, Y. V. Grinkova, C. Ho, T. Kim, D. Muller, S. Sligar, T. Sorsch, R. Twesten, R. Timp, and G. Timp. 2003. The detection of DNA using a silicon nanopore. IEDM '03 Technical Digest. IEEE International, 8-10 Dec. 2003. 32.2.1-32.2.4.
20. 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 an artificial nanopore. Biophys. J. In press.
21. Howorka, S., S. Cheley, and H. Bayley. 2001. Sequence-specific detection of individual DNA strands using engineered nanopores. Nat. Biotechnol. 19:636-639.
22. Hummer, G., J. C. Rasaiah, and J. P. Noworyta. 2001. Water conduction through the hydrophobic channel of a carbon nanotube. Nature. 414:188-190.
23. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14:33-38.
24. 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. Comp. Phys. 151:283-312.
25. Kasianowicz, J. J., E. Brandib, D. Branton, and W. Deamer. 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA. 93:13770-13773.
26. Kong, C. Y., and M. Muthukumar. 2002. Modeling of polynucleotide translocation through protein pores and nanotubes. Electrophoresis. 23:2697-2703.
27. 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.
28. Li, J., D. Stein, C. McMullan, D. Branton, M. J. Aziz, and J. A. Golovchenko. 2001. Ion-beam sculpting at nanometre length scales. Nature. 412:166-169.
29. Loebl, H. C., R. Randel, S. P. Goodwin, and C. C. Matthai. 2003. Simulation studied of polymer translocation through a channel. Phys. Rev. E. Stat. Nonlin. Soft Matter. Phys. 67:041913.
30. Lopez, C. F., S. O. Nielsen, P. B. Moore, and M. L. Klein. 2004. Understanding nature's design for a nanosyringe. Proc. Natl. Acad. Sci. USA. 101:4431-4434.
31. Lubensky, D. K., and D. R. Nelson. 1999. Driven polymer translocation through a narrow pore. Biophys. J. 77:1824-1838.
32. MacKerell, A. D., Jr., B. Brooks, C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998. CHARMM: the energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry. P. Schleyer, editor. John Wiley & Sons, Chichester, UK. 271-277.
33. Mara, A., Z. Siwy, C. Trautmann, J. Wan, and F. Kamme. 2004. An asymmetric polymer nanopore for single molecule detection. Nano. Lett. 4:497-501.
34. Martyna, G. J., D. J. Tobias, and M. L. Klein. 1994. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101:4177-4189.
35. Matzler, R., and J. Klafter. 2003. When translocation dynamics becomes anomalous. Biophys. J. 85:2776-2779.
36. Meller, A. 2003. Dynamics of polynucleotide transport through nanometre-scale pores. J. Phys. Condens. Matter. 15:R581-R607.
37. Meller, A., L. Nivon, E. Brandin, J. Golovchenko, and D. Branton. 2000. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. USA. 97:1079-1084.
38. Muthukumar, M. 1999. Polymer translocation through a hole. J. Chem. Phys. 111:10371-10374.
39. Muthukumar, M. 2001. Translocation of a confined polymer through a hole. Phys. Rev. Lett. 86:3188-3191.
40. Muthukumar, M. 2003. Polymer escape through a nanopore. J. Chem. Phys. 118:5174-5184.
41. Polygen. 1988. Quanta. Polygen Corporation, Waltham, MA.
42. + conduction in the single-file water chain of the gramicidin channel. Biophys. J. 82:2304-2316.
43. Slonkina, E., and A. B. Kolomeisky. 2003. Polymer translocation through a long nanopore. J. Chem. Phys. 118:7112-7118.
44. Song, L., M. R. Hobaugh, C. Shustak, S. Cheley, H. Bayley, and J. E. Gouaux. 1996. Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore. Science. 274:1859-1866.
45. Storm, A. J., J. H. Chen, X. S. Ling, H. W. Zandergen, and C. Dekker. 2003. Fabrication of solid-state nanopore with single-nanometre precision. Nat. Mater. 2:537-540.
46. Sung, S.-S., and X.-W. Wu. 1996. Molecular dynamics simulations of synthetic peptide folding. Proteins Struct. Func. Genet. 25:202-214.
47. Tajkhorshid, E., P. Nollert, M. Ø. Jensen, L. J. W. Miercke, J. O'Connell, R. M. Stroud, and K. Schulten. 2002. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science. 296:525-530.
48. Vercoutere, W. A., S. Winters-Hilt, V. S. DeGuzman, D. Deamer, S. E. Ridino, J. T. Rodgers, H. E. Olsen, A. Marziali, and M. Akeson. 2003. Discrimination among individual Watson-Crick basepairs at the termini of single DNA hairpin molecules. Nucleic Acids Res. 31:1311-1318.
49. Vercoutere, W., S. Winters-Hilt, H. Olsen, D. Deamer, D. Haussler, and M. Akeson. 2001. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat. Biotechnol. 19:248-252.
50. 4. J. Chem. Phys. 97:5048-5062.
51. Wong, K. Y., and B. M. Pettitt. 2001. A study of DNA tethered to a surface by an all-atom molecular dynamics simulation. Theo. Chem. Accounts. 106:233-235.
52. Yeh, I. C., and G. Hummer. 2004. Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophys. J. 86:681-689.
53. Zhu, F., E. Tajkhorshid, and K. Schulten. 2002. Pressure-induced water transport in membrane channels studied by molecular dynamics. Biophys. J. 83:154-160.