Base-by-base ratcheting of single stranded DNA through a solid-state nanopore

Physical Review Letters

Volumn 104, Issue 23, 2010, Pages

  Luan, Binquan ^a   Peng, Hongbo ^a   Polonsky, Stas ^a   Rossnagel, Steve ^a   Stolovitzky, Gustavo ^a   Martyna, Glenn ^a  

^a IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMISTIC DYNAMICS; DNA SENSING; ELECTROSTATIC TRAP; LANGEVIN; MOLECULAR DYNAMICS SIMULATIONS; PHOSPHATE GROUP; SIMULATION RESULT; SIMULATION TIME; SINGLE-STRANDED DNA; SINGLE-STRANDED DNA (SS-DNA); SOLID-STATE NANOPORE; STEP SIZE; TIME-SCALES; TRANSLOCATION DYNAMICS;

DNA; DYNAMICS; GENES; MOLECULAR DYNAMICS; NANOPORES; SIGNAL TO NOISE RATIO;

COMPUTER SIMULATION;

EID: 77953529031     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.104.238103     Document Type: Article

References (30)

1. J. Li, M. Gershow, D. Stein, E. Brandin, and J.A. Golovchenko, Nature Mater. 2, 611 (2003). NMAACR 1476-1122 10.1038/nmat965
2. C. Dekker, Nature Nanotech. 2, 209 (2007). 1748-3387 10.1038/nnano.2007. 27
3. D. Branton, D. Deamer, A. Marziali, H. Bayley, S. Benner, T. Butler, M. Di Ventra, S. Garaj, A. Hibbs, and X.e.a. Huang, Nat. Biotechnol. NABIF9 1087-0156 26, 1146 (2008). 10.1038/nbt.1495
4. M. Wanunu, W. Morrison, Y. Rabin, A.Y. Grosberg, and A. Meller, Nature Nanotech. 5, 160 (2010). 1748-3387 10.1038/nnano.2009.379
5. K. Luo, T. Ala-Nissila, S. Ying, and A. Bhattacharya, Phys. Rev. Lett. 100, 058101 (2008). PRLTAO 0031-9007 10.1103/PhysRevLett.100.058101
6. D. Lubensky and D. Nelson, Biophys. J. 77, 1824 (1999). BIOJAU 0006-3495 10.1016/S0006-3495(99)77027-X
7. J. Lagerqvist, M. Zwolak, and M.D. Ventra, Nano Lett. 6, 779 (2006). NALEFD 1530-6984 10.1021/nl0601076
8. M. Gracheva, A. Aksimentiev, and J.-P. Leburton, Nanotechnology 17, 3160 (2006). NNOTER 0957-4484 10.1088/0957-4484/17/13/014
9. J.J. Kasianowicz, E. Brandin, D. Branton, and D.W. Deamer, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 93, 13770 (1996). 10.1073/pnas.93.24.13770
10. S. Iqbal, D. Akin, and R. Bashir, Nature Nanotech. 2, 243 (2007). 1748-3387 10.1038/nnano.2007.78
11. S. Chang, J. He, A. Kibel, M. Lee, O. Sankey, P. Zhang, and S. Lindsay, Nature Nanotech. 4, 297 (2009). 1748-3387 10.1038/nnano.2009.48
12. A. Meller, L. Nivon, E. Brandin, J. Golovchenko, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 97, 1079 (2000). 10.1073/pnas.97.3.1079
13. D. Fologea, J. Uplinger, B. Thomas, D.S. McNabb, and J. Li, Nano Lett. 5, 1734 (2005). NALEFD 1530-6984 10.1021/nl051063o
14. B.Q. Luan and A. Aksimentiev, Phys. Rev. E PLEEE8 1539-3755 78, 021912 (2008). 10.1103/PhysRevE.78.021912
15. S. Ghosal, Phys. Rev. E PLEEE8 1539-3755 76, 061916 (2007). 10.1103/PhysRevE.76.061916
16. S. van Dorp, U. Keyser, N. Dekker, C. Dekker, and S. Lemay, Nature Phys. 5, 347 (2009). NPAHAX 1745-2473 10.1038/nphys1230
17. G. Sigalov, J. Comer, G. Timp, and A. Aksimentiev, Nano Lett. 8, 56 (2008). NALEFD 1530-6984 10.1021/nl071890k
18. H. Peng and X. Ling, Nanotechnology 20, 185101 (2009). NNOTER 0957-4484 10.1088/0957-4484/20/18/185101
19. U. Keyser, B. Koeleman, S. Dorp, D. Krapf, R. Smeets, S. Lemay, N. Dekker, and C. Dekker, Nature Phys. 2, 473 (2006). NPAHAX 1745-2473 10.1038/nphys344
20. A. Schirmeisen, D. Weiner, and H. Fuchs, Phys. Rev. Lett. 97, 136101 (2006). PRLTAO 0031-9007 10.1103/PhysRevLett.97.136101
21. S. Polonsky, S. Rossnagel, and G. Stolovitzky, Appl. Phys. Lett. 91, 153103 (2007). APPLAB 0003-6951 10.1063/1.2798247
22. C. Ke, M. Humeniuk, H. S-Gracz, and P.E. Marszalek, Phys. Rev. Lett. 99, 018302 (2007). PRLTAO 0031-9007 10.1103/PhysRevLett.99.018302
23. M. Wanunu and A. Meller, Nano Lett. 7, 1580 (2007). NALEFD 1530-6984 10.1021/nl070462b
24. B.Q. Luan, H. Peng, S. Polonsky, S. Rossnagel, G. Stolovitzky, and G. Martyna (unpublished).
25. D.B. Wells, V. Abramkina, and A. Aksimentiev, J. Chem. Phys. 127, 125101 (2007). JCPSA6 0021-9606 10.1063/1.2770738
26. J.C. Phillips,, J. Comput. Chem. JCCHDD 0192-8651 26, 1781 (2005). 10.1002/jcc.20289
27. A. Perez, I. Marchan, D. Svozil, J. Sponer, T.E. Cheatham, C.A. Laughton, and M. Orozco, Biophys. J. 92, 3817 (2007). BIOJAU 0006-3495 10.1529/biophysj.106.097782
28. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, J. Chem. Phys. 79, 926 (1983). JCPSA6 0021-9606 10.1063/1.445869
29. J. Moffitt, Y. Chemla, D. Izhaky, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 9006 (2006). 10.1073/pnas.0603342103
30. R. Zwanzig, in Nonequilibrium Statistic Mechanics, (Oxford University Press, New York, 2001).