Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix

Nanotechnology

Volumn 21, Issue 39, 2010, Pages

  Mirsaidov, Utkur ^a   Comer, Jeffrey ^a,b   Dimitrov, Valentin ^a   Aksimentiev, Aleksei ^a,b   Timp, Gregory ^a,c  

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

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

^c UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANONICAL STRUCTURE; DOUBLE HELIX; DOUBLE STRANDED DNA; DOUBLE-STRANDED DNA (DS-DNA); ELECTRIC FORCE; HIGH FIDELITY; HIGH RESOLUTION; MOLECULAR DYNAMICS SIMULATIONS; SINGLE MOLECULE; SOLID-STATE MEMBRANES;

ELECTRIC FIELDS; MOLECULAR DYNAMICS;

NANOPORES;

DNA; VIRUS DNA;

ARTICLE; BACTERIOPHAGE LAMBDA; CHEMISTRY; CONFORMATION; ELECTROCHEMICAL ANALYSIS; METHODOLOGY; MOLECULAR DYNAMICS; NANOPORE; NANOTECHNOLOGY; PARTICLE SIZE; TRANSMISSION ELECTRON MICROSCOPY; ULTRASTRUCTURE;

BACTERIOPHAGE LAMBDA; DNA; DNA, VIRAL; ELECTROCHEMICAL TECHNIQUES; MICROSCOPY, ELECTRON, TRANSMISSION; MOLECULAR DYNAMICS SIMULATION; NANOPORES; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; PARTICLE SIZE;

EID: 77958593282     PISSN: 09574484     EISSN: 13616528     Source Type: Journal    
DOI: 10.1088/0957-4484/21/39/395501     Document Type: Article

References (28)

1. Ashkin A 1997 Optical trapping and manipulation of neutral particles using lasers Natl Acad. Sci. 94 4853-60
2. Krüger P, Luo X, Klein M W, Brugger K, Haase A, Wildermuth S, Groth S, Bar-Joseph I, Folman R and Schmiedmayer J 2003 Trapping and manipulating neutral atoms with electrostatic fields Phys. Rev. Lett. 91 233201
3. Meek S A, Bethlem H L, Conrad H and Meijer G 2008 Trapping molecules on a chip in traveling potential wells Phys. Rev. Lett. 100 153003
4. Branton D et al 2008 The potential and challenges of nanopore sequencing Nat. Biotechnol. 26 1146-53
5. Mirsaidov U, Timp W, Zou X, Dimitrov V, Schulten K, Feinberg A P and Timp G 2009 Nanoelectromechanics of methylated DNA in a synthetic nanopore Biophys. J. 96 L32-43
6. Zhao Q, Comer J, Dimitrov V, Yemenicioglu S, Aksimentiev A and Timp G 2008 Stretching and unzipping nucleic acid hairpins using a synthetic nanopore Nucleic Acids Res. 36 1532-41
7. Lederer H, May R P, Kjems J K, Baer G and Heumann H 1986 Solution structure of a short DNA fragrment studied by neutron-scattering Eur. J. Biochem. 161 191-6
8. Heng J B, Aksimentiev A, Ho C, Marks P, Grinkova Y V, Sligar S, Schulten K and Timp G 2005 Stretching DNA using the electric field in a synthetic nanopore Nano Lett. 5 1883-8
9. Heng J B, Aksimentiev A, Ho C, Marks P, Grinkova Y V, Sligar S, Schulten K and Timp G 2006 The electromechanics of DNA in a synthetic nanopore Biophys. J. 90 1098-106
10. Comer J, Dimitrov V, Zhao Q, Timp G and Aksimentiev A 2009 Microscopic mechanics of hairpin DNA translocation through synthetic nanopores Biophys. J. 96 593-608
11. Timp W, Mirsaidov U M, Wang D, Comer J, Aksimentiev O and Timp G 2010 Nanopore sequencing: electrical measurements of the code of life IEEE Trans. Nanotechnol. 9 281-94
12. Mirsaidov U M, Wang D, Timp W and Timp G 2010 Molecular diagnostics for personal medicine using a nanopore Wires Rev. Nanomed. Nanobiotechnol. 2 367-81
13. Ho C, Qiao R, Heng J B, Chatterjee A, Timp R J, Aluru N R and Timp G 2005 Electrolytic transport through a synthetic nanometer-diameter pore Proc. Natl Acad. Sci. USA 102 10445-50
14. Dimitrov V, Mirsaidov U, Wang D, Sorsch T, Mansfield W, Miner J, Klemens F, Cirelli R, Yemenicioglu S and Timp G 2010 Nanopores in solid-state membranes engineered for single molecule detection Nanotechnology 21 065502
15. Smeets R M M, Keyser U F, Dekker N H and Dekker C 2008 Noise in solid-state nanopores Proc. Natl Acad. Sci. USA 105 417-21
16. Aksimentiev A, Heng J B, Timp G and Schulten K 2004 Microscopic kinetics of DNA translocation through synthetic nanopores Biophys. J. 87 2086-97
17. Aksimentiev A 2010 Deciphering ionic current signatures of DNA transport through a nanopore Nanoscale 2 468-83
18. Cruz-Chu E R, Aksimentiev A and Schulten K 2006 Water-silica force field for simulating nanodevices J. Phys. Chem. B 110 21497-508
19. Vanbeest B W H, Kramer G J and Vansanten R A 1990 Force-fields for silicas and aluminophosphates based on ab initio calculations Phys. Rev. Lett. 64 1955-8
20. Vollmayr K, Kob W and Binder K 1996 Cooling-rate effects in amorphous silica: a computer-simulation study Phys. Rev. B 54 15808-27
21. Wells D B, Abramkina V and Aksimentiev A 2007 Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics J. Chem. Phys. 127 125101
22. 4J. Chem. Phys. 97 5048-62
23. Goychuk I and Hanggi P 2002 Ion channel gating: a first-passage time analysis of the Kramers type Proc. Natl Acad. Sci. USA 99 3552-6
24. Fologea D, Uplinger J, Thomas B, McNabb D S and Li J L 2005 Slowing DNA translocation in a solid-state nanopore Nano Lett. 5 1734-7
25. Storm A J, Storm C, Chen J H, Zandbergen H, Joanny J F and Dekker C 2005 Fast DNA translocation through a solid-state nanopore Nano Lett. 5 1193-7
26. Smeets R, Dekker N and Dekker C 2009 Low-frequency noise in solid-state nanopores Nanotechnology 20 095501
27. Wang D, Shim J, Timp W, Mirsaidov U, Comer J, Aksimentiev A and Timp G 2010 Nat. Nanotechnol. submitted
28. Pop M and Salzberg S L 2008 Bioinformatics challenges in new sequencing technologies Trends Genet. 24 142-9