DNA base pair resolution by single molecule force spectroscopy

Nucleic Acids Research

Volumn 32, Issue 16, 2004, Pages 4876-4883

  Sattin, Bernie D ^a   Pelling, Andrew E ^a,b   Goh, M Cynthia ^a  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; COMPLEMENTARY DNA; OLIGONUCLEOTIDE; PROTEIN; THYMINE; DNA; OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; ATOMIC FORCE MICROSCOPY; BASE MISPAIRING; BASE PAIRING; CONTROLLED STUDY; DNA HELIX; DNA MICROARRAY; DNA STRAND; FORCE; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DNA BINDING; SENSITIVITY AND SPECIFICITY; SPECTROSCOPY; CHEMISTRY; EVALUATION; METHODOLOGY;

BASE PAIR MISMATCH; BASE PAIRING; DNA; HYDROGEN BONDING; MICROSCOPY, ATOMIC FORCE; OLIGODEOXYRIBONUCLEOTIDES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPECTRUM ANALYSIS;

EID: 4444378983     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh826     Document Type: Article

References (35)

1. Breslauer,K.J. (1995) Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods Enzymol., 259, 221-242.
2. Breslauer,K.J., Frank,R., Blocker,H. and Marky,L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
3. Chalikian,T.V., Volker,J., Plum,G.E. and Breslauer,K.J. (1999) A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques. Proc. Natl Acad. Sci. USA, 96, 7853-7858.
4. Rouzina,I. and Bloomfield,V.A. (1999) Heat capacity effects on the melting of DNA. 1. General aspects. Biophys. J., 77, 3242-3251.
5. Rouzina,I. and Bloomfield,V.A. (1999) Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects. Biophys. J., 77, 3252-3255.
6. Bockelmann,U., EssevazRoulet,B. and Heslot,F. (1997) Molecular stick-slip motion revealed by opening DNA with picoNewton forces. Phys. Rev. Lett., 79, 4489-4492.
7. Zhang,Y., Zhou,H.J. and Ou-Yang,Z.C. (2001) Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions. Biophys. J., 81, 1133-1143.
8. Rouzina,I. and Bloomfield,V.A. (2001) Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys. J., 80, 882-893.
9. Rief,M., Clausen-Schaumann,H. and Gaub,H.E. (1999) Sequence-dependent mechanics of single DNA molecules. Nature Struct. Biol., 6, 346-349.
10. Clausen-Schaumann,H., Rief,M., Tolksdorf,C. and Gaub,H.E. (2000) Mechanical stability of single DNA molecules. Biophys. J., 78, 1997-2007.
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. Lee,G.U., Chrisey,L.A. and Colton,R.J. (1994) Direct measurement of the forces between complementary strands of DNA. Science, 266, 771-773.
13. MacKerell,A.D. and Lee,G.U. (1999) Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads. Eur. Biophys. J., 28, 415-426.
14. Noy,A., Vezenov,D.V., Kayyem,J.F., Meade,T.J. and Lieber,C.M. (1997) Stretching and breaking duplex DNA by chemical force microscopy. Chem. Biol., 4, 519-527.
15. Pope,L.H., Davies,M.C., Laughton,C.A., Roberts,C.J., Tendler,S.J. and Williams,P.M. (2001) Force-induced melting of a short DNA double helix. Eur. Biophys. J., 30, 53-62.
16. 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.
17. Schumakovitch,I., Grange,W., Strunz,T., Bertoncini,P., Guntherodt,H.J. and Hegner,M. (2002) Temperature dependence of unbinding forces between complementary DNA strands. Biophys. J., 82, 517-521.
18. Boland,T. and Ratner,B.D. (1995) Direct measurement of hydrogen-bonding in DNA nucleotide bases by atomic-force microscopy. Proc. Natl Acad. Sci. USA, 92, 5297-5301.
19. Gibson,C.T., Watson,G.S. and Myhra,S. (1996) Determination of the spring constants of probes for force microscopy/spectroscopy. Nanotechnology, 7, 259-262.
20. Cleveland,J.P., Manne,S., Bocek,D. and Hansma,P.K. (1993) A nondestructive method for determining the spring constant of cantilevers for scanning force microscopy. Rev. Sci. Instrum., 64, 403-405.
21. Hutter,J.L. and Bechhoefer,J. (1993) Calibration of atomic-force microscope tips. Rev. Sci. Instrum., 64, 1868-1873.
22. Senden,T.J. and Ducker,W.A. (1994) Experimental-determination of spring constants in atomic-force microscopy. Langmuir, 10, 1003-1004.
23. Butt,H.J. and Jaschke,M. (1995) Calculation of thermal noise in atomic-force microscopy. Nanotechnology, 6, 1-7.
24. Sader,J.E., Larson,I., Mulvaney,P. and White,L.R. (1995) Method for the calibration of atomic-force microscope cantilevers. Rev. Sci. Instrum., 66, 3789-3798.
25. Sam,M., Boon,E.M., Barton,J.K., Hill,M.G. and Spain,E.M. (2001) Morphology of 15mer duplexes tethered to Au(111) probed using scanning probe microscopy. Langmuir, 17, 5727-5730.
26. Mourougou-Candoni,N., Naud,C. and Thibaudau,F. (2003) Adsorption of thiolated oligonucleotides on gold surfaces: an atomic force microscopy study. Langmuir, 19, 682-686.
27. Markiewicz,P. and Goh,M.C. (1997) Identifying locations on a substrate for the repeated positioning of AFM samples. Ultramicroscopy 68, 215-221.
28. Peyret,N., Seneviratne,P.A., Allawi,H.T. and SantaLucia,J. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A center dot A, C center dot C, G center dot G, and T center dot T mismatches. Biochemistry, 38, 3468-3477.
29. SantaLucia,J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
30. Wang,J. and Bard,A.J. (2001) Monitoring DNA immobilization and hybridization on surfaces by atomic force microscopy force measurements. Anal. Chem., 73, 2207-2212.
31. Evans,E. and Ritchie,K. (1999) Strength of a weak bond connecting flexible polymer chains. Biophys. J., 76, 2439-2447.
32. Grange,W., Strunz,T., Schumakovitch,I., Guntherodt,H. and Hegner,M. (2001) Molecular recognition and adhesion of individual DNA strands studied by dynamic force microscopy. Single Molecules, 2 75-78.
33. Bockelmann,U., Thomen,P., Essevaz-Roulet,B., Viasnoff,V. and Heslot,F. (2002) Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys. J., 82, 1537-1553.
34. Delaney,J.C., Henderson,P.T., Helquist,S.A., Morales,J.C., Essigmann,J.M. and Kool,E.T. (2003) High-fidelity in vivo replication of DNA base shape mimics without Watson-Crick hydrogen bonds. Proc. Natl Acad. Sci. USA, 100, 4469-4473.
35. Kool,E.T. (2001) Hydrogen bonding, base stacking, and steric effects in DNA replication. Annu. Rev. Biophys. Biomol. Struct., 30, 1-22.