Stretching and unzipping nucleic acid hairpins using a synthetic nanopore

Nucleic Acids Research

Volumn 36, Issue 5, 2008, Pages 1532-1541

  Zhao, Q ^a   Comer, J ^a   Dimitrov, V ^a   Yemenicioglu, S ^a   Aksimentiev, A ^a   Timp, G ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

DNA; SILICON NITRIDE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DNA STRUCTURE; ELECTRIC FIELD; ELECTRIC POTENTIAL; MOLECULAR DYNAMICS; NANOELECTROMECHANICAL SYSTEM; NANOPORE; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SCANNING TRANSMISSION ELECTRON MICROSCOPY; SIMULATION;

BIOLOGICAL TRANSPORT; DNA; ELECTRIC CONDUCTIVITY; MEMBRANES, ARTIFICIAL; MODELS, MOLECULAR; NANOSTRUCTURES; NUCLEIC ACID CONFORMATION; SILICON COMPOUNDS;

EID: 41149161730     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm1017     Document Type: Article

References (42)

1. Stryer,L. (1999) Biochemistry W.H. Freeman and Co., New York.
2. Essevaz-Roulet,B., Bockelmann,U. and Heslot,F. (1997) Mechanical separation of the complementary strands of DNA. Proc. Natl Acad. Sci. USA, 94, 11935-11940.
3. Rief,M., Clausen-Schaumann,H. and Gaub,H.E. (1999) Sequence-dependent mechanics of single DNA molecule. Nat. Struct. Biol, 6, 346-349.
4. Woodside,M.T., Behnke-Parks,W.M., Larizadeh,K., Travers,K., Herschlag,D. and Bloch,S.M. (2006) Nanomechanical measurement of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc. Natl Acad. Sci. USA, 103, 6190-6195.
5. Williams,M.C. Optical Tweezers: Measuring PicoNewton Forces. Biophysical Text Book On-line (BPOL), http://www.biophysics.org/education/ techniques.html (2004).
6. McCauley,M.J. and Williams,M.C. (2007) Mechanisms of DNA binding determined in optical tweezers experiments. Biopolymers, 85, 154-168.
7. Strunz,T., Oroszlan,K., Schafer,R. and Guntherodt,H.-J. (1999) Dynamic force spectroscopy of single DNA molecules. Proc. Natl Acad. Sci. USA 96, 11277-11282.
8. Liphart,J., Onoa,B., Smith,B., Tinoco, and Bustamante,C. (2001) Reversible unfolding of single RNA molecules by mechanical force. Science, 292, 733-737.
9. Rouzina,I. and Bloomfield,V.A. (2001) Force induced melting of DNA: thermodynamic analysis. Biophys. J., 80, 882-883.
10. 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, 1098-1106.
11. Bustamante,C., Smith,S.B., Liphardt,J. and Smith,D. (2000) Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol., 10, 279-285.
12. Cluzel-Schaumann,H., Rief,M., Tolksdorf,C. and Gaub,H.E. (2000) Mechanical stability of single DNA molecules. Biophys. J., 78, 1997-2007.
13. 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, 1883-1888.
14. Mathé,J., Visram,H., Viasnoff,V., Rabin,Y. and Meller,A. (2006) Nanopore unzipping of individual DNA hairpin molecules. Biophys. J. 87, 3205-3212
15. and Mathé,J., Arinstein,A., Rabin,Y. and Meller,A. (2006) Equilibrium and irreversible unzipping of DNA in a nanopore. Europhys. Lett., 73 128.
16. Vercoutere,W., Winters-Hilt,S., Olsen,H., Deamer,D., Haussler,D. and Akeson,M. (2001) Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat. Biotech., 19, 248-252.
17. Zhao,Q., Sigalov,G., Dimitrov,V., Dorvel,B., Mirsaidov,U., Sligar,S., Aksimentiev,A. and Timp,G. (2007) Genotyping with a synthetic nanopore. Nano Lett., 7, 1680-1685.
18. Tropini,C. and Marziali,A. (2007) Multi-nanopore force spectroscopy for DNA analysis. Biophys. J., 92, 1632-1637.
19. Keyser,U.F., Koelemean,B.N., VanDorp,S., Krapf,D., Smeets,R.M.M., Lemay,S.G., Dekker,N.H. and Dekker,C. (2006) Direct force measurements of DNA in a solid-state nanopore. Nat. Phys., 2, 473-475.
20. Ho,C., Qiao,R., Heng,J., Chatterjee,A., Timp,R., Aluru,N. and Timp,G. (2005) Electrolytic transport through a synthetic nanometer-diameter pore. Proc. Natl. Acad. Sci. USA, 102, 10445-10450.
21. Bonnet,G., Krichevsky,O. and Libchaber,A. (1998) Kinetics of conformation fluctuations in DNA hairpin-loops. Proc. Natl Acad. Sci. USA, 95, 8602-8606.
22. Serra,M.J. and Turner,D.H. (1995) Predicting thermodynamic properties of RNA. Methods Enzymol., 259, 242-261.
23. Wartell,R.M. and Benight,A.S. (1985) Thermal denaturation of DNA molecules: A comparison of theory and experiment. Phys. Rep., 126, 67.
24. Goddard,N.L., Bonnet,G, Krichevsky,O. and Libchaber,A. (2000) Sequence- dependent rigidity of single stranded DNA. Proc. Natl Acad. Sci. USA 95, 8602-8606.
25. Siwy,Z. (2006) Ion-current rectification in nanopores and nanotubes with broken symmetry. Adv. Funct. Mat., 16, 735-746.
26. Siwy,Z. and Fuliński,A. (2002) Fabrication of a synthetic nanopore ion pump. Phys. Rev. Lett., 89, 198103-198106.
27. Doose,S., Barsch,H. and Sauer,M. (2007) Polymer properties of polythymine as reveal by translational diffusion. Biophys. J., 93, 1224-1234.
28. Saenger,W. (1983) Principles of Nucleic Acid Structure Wolfram Saenger, Springer-Verlag, New York.
29. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
30. Mathews,D.H., Sabina,J, Zuker,M. and Turner,D.H. (1999) Expanded sequence dependenceof thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol, 288, 911-940.
31. Heng J.B., Ho,C., Kim,T., Timp,R., Aksimentiev,A., Grinkova,Y.V., Sligar,S., Schulten,K. and Timp,G. (2004) Sizing DNA using a nanometer-diameter pore. Biophys. J., 87, 2905-2911.
32. Aksimentiev,A., Heng,J.B., Timp,G. and Schulten,K. (2004) Microscopic kinetics of DNA translocation through synthetic nanopores. Biophys. J., 87, 2086-2097.
33. Phillips,J.C., Braun, R., Wang,W., Gumbart,J., Tajkhorshid,E., Villa,E., Chipot,C., Skeel,R. D., Kalé,L. et al. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem., 26, 1781-1802.
34. Batcho,P.F., Case,D.A. and Schlick, T. (2001) Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. J. Chem. Phys., 115, 4003-4018.
35. 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,H., Kollman,P.A. et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc, 117, 5179-5197.
36. Martyna,G. J., Tobias,D.J. and Klein,M.L. (1994) Constant-pressure molecular-dynamics algorithms. J. Chem. Phys., 101, 4177-4189.
37. Izrailev,S., Stepaniants,S., Balsera,M., Oono,Y. and Schulten, K. (1997) Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J., 72, 1568-1581.
38. Storm,A. J., Chen,J.H., Zandbergen,H.W. and Dekker,C. (2005) Translocation of double-strand DNA through a silicon oxide nanopore. Phys. Rev. E, 71, 051903-051912.
39. Chen,P., Gu,J., Brandin,E., Kim,Y.-R., Wang,Q. and Branton,D. (2004) Probing single DNA molecule transport using fabricated nanopores. Nano Lett., 4, 2293-2298.
40. Nakane,J., Akeson,M. and Marziali,A. (2002) Evaluation of nanopores as candidates for electronic analyte detection. Electrophoresis, 23, 2592-2601.
41. Chang,H., Kosari,F., Andreadakis,G., Alam,M.A., Vasmatzis,G. and Bashir,R. (2004) DNA-mediated fluctuations in the ionic current through silicon oxide nanopore channels. Nano Lett., 4, 1551-1556.
42. Folgea,D., Uplinger,J., Thomas,B., McNabb, D.S. and Li,J. (2005) Slowing DNA translocation in a solid-state nanopore. Nano Lett., 5, 1734-1737.