Direct measurements of base stacking interactions in DNA by single-molecule atomic-force spectroscopy

Physical Review Letters

Volumn 99, Issue 1, 2007, Pages

  Ke, Changhong ^a   Humeniuk, Michael ^a   S Gracz, Hanna ^b   Marszalek, Piotr E ^a  

^a Duke University   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC FORCE MICROSCOPY; ELASTICITY; MOLECULAR INTERACTIONS; NUCLEOTIDES;

ADENINES; BASE STACKING INTERACTIONS;

DNA;

EID: 34547243940     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.99.018302     Document Type: Article

References (42)

1. C. Bustamante, Z. Bryant, and S.B. Smith, Nature (London) 421, 423 (2003). NATUAS 0028-0836 10.1038/nature01405
2. S.B. Smith, Y.J. Cui, and C. Bustamante, Science 271, 795 (1996). SCIEAS 0036-8075 10.1126/science.271.5250.795
3. J. Gore, Z. Bryant, M. Nöllmann, M.U. Le, N.R. Cozzarelli, and C. Bustamante, Nature (London), 442, 836 (2006). NATUAS 0028-0836 10.1038/nature04974
4. C. Bustamante, J.F. Marko, E.D. Siggia, and S. Smith, Science 265, 1599 (1994). SCIEAS 0036-8075 10.1126/science.8079175
5. G.J.L. Wuite, S.B. Smith, M. Young, D. Keller, and C. Bustamante, Nature (London) 404, 103 (2000). NATUAS 0028-0836 10.1038/35003614
6. C.G. Baumann, S.B. Smith, V.A. Bloomfield, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 94, 6185 (1997). 10.1073/pnas.94.12.6185
7. J.R. Wenner, M.C. Williams, I. Rouzina, and V.A. Bloomfield, Biophys. J. 82, 3160 (2002). BIOJAU 0006-3495
8. M.C. Williams, J.R. Wenner, I. Rouzina, and V.A. Bloomfield, Biophys. J. 80, 1932 (2001). BIOJAU 0006-3495
9. I. Rouzina and V.A. Bloomfield, Biophys. J. 80, 882 (2001). BIOJAU 0006-3495
10. M.D. Wang, H. Yin, R. Landick, J. Gelles, and S.M. Block, Biophys. J. 72, 1335 (1997). BIOJAU 0006-3495
11. J.F. Marko, Phys. Rev. E 57, 2134 (1998). PLEEE8 1063-651X 10.1103/PhysRevE.57.2134
12. J.F. Leger, G. Romano, A. Sarkar, J. Robert, L. Bourdieu, D. Chatenay, and J.F. Marko, Phys. Rev. Lett. 83, 1066 (1999). PRLTAO 0031-9007 10.1103/PhysRevLett.83.1066
13. S. Cocco, J. Yan, J.F. Leger, D. Chatenay, and J.F. Marko, Phys. Rev. E PLEEE8 1063-651X 70, 011910 (2004). 10.1103/PhysRevE.70.011910
14. M.C. Williams, J.R. Wenner, L. Rouzina, and V.A. Bloomfield, Biophys. J. 80, 874 (2001). BIOJAU 0006-3495
15. P. Cluzel, A. Lebrun, C. Heller, R. Lavery, J.L. Viovy, D. Chatenay, and F. Caron, Science 271, 792 (1996). SCIEAS 0036-8075 10.1126/science.271.5250.792
16. S. Cocco, J.F. Marko, R. Monasson, A. Sarkar, and J. Yan, Eur. Phys. J. E EPJSFH 1292-8941 10, 249 (2003). 10.1140/epje/i2002-10113-2
17. M.N. Dessinges, B. Maier, Y. Zhang, M. Peliti, D. Bensimon, and V. Croquette, Phys. Rev. Lett. 89, 248102 (2002). PRLTAO 0031-9007 10.1103/PhysRevLett.89.248102
18. Y. Seol, G.M. Skinner, and K. Visscher, Phys. Rev. Lett. 93, 118102 (2004). PRLTAO 0031-9007 10.1103/PhysRevLett.93.118102
19. Y. Zhang, H. Zhou, and Z.-C. Ou-Yang, Biophys. J. 81, 1133 (2001). BIOJAU 0006-3495
20. H. Clausen-Schaumann, M. Rief, C. Tolksdorf, and H.E. Gaub, Biophys. J. 78, 1997 (2000). BIOJAU 0006-3495
21. D.H. Turner, in Nucleic Acids: Structure Properties and Functions, edited by, V.A. Bloomfield, D.M. Crothers, and, I. Tinoco, Conformational Changes (University Science Books, Sausalito, California, 2000), pp. 259-334.
22. D.P. Aalberts, J.M. Parman, and N.L. Goddard, Biophys. J. 84, 3212 (2003). BIOJAU 0006-3495
23. A. Sain, B.-Y. Ha, H.-K. Tsao, and J.Z.Y. Chen, Phys. Rev. E PLEEE8 1063-651X 69, 061913 (2004). 10.1103/PhysRevE.69.061913
24. A. Buhot and A. Halperin, Phys. Rev. E PLEEE8 1063-651X 70, 020902 (2004). 10.1103/PhysRevE.70.020902
25. W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, Berlin, 1984).
26. J.B. Mills, E. Vacano, and P.J. Hagerman, J. Mol. Biol. 285, 245 (1999). JMOBAK 0022-2836 10.1006/jmbi.1998.2287
27. A. Sain, B.Y. Ha, H.K. Tsao, and J.Z.Y. Chen, Phys. Rev. E 69, 061913 (2004). PLEEE8 1063-651X 10.1103/PhysRevE.69.061913
28. N.L. Goddard, G. Bonnet, O. Krichevsky, and A. Libchaber, Phys. Rev. Lett. 85, 2400 (2000). PRLTAO 0031-9007 10.1103/PhysRevLett.85.2400
29. K.R. Hagerman and P.J. Hagerman, J. Mol. Biol. 260, 207 (1996). JMOBAK 0022-2836 10.1006/jmbi.1996.0393
30. Y. Seol, G.M. Skinner, K. Visscher, A. Buhot, and A. Halperin, Phys. Rev. Lett. 98, 158103 (2007). PRLTAO 0031-9007 10.1103/PhysRevLett.98.158103
31. G. Lee, K. Abdi, Y. Jiang, P. Michaely, V. Bennett, and P.E. Marszalek, Nature (London) 440, 246 (2006). NATUAS 0028-0836 10.1038/nature04437
32. P.E. Marszalek, A.F. Oberhauser, Y.P. Pang, and J.M. Fernandez, Nature (London) 396, 661 (1998). NATUAS 0028-0836 10.1038/25322
33. E.L. Florin, M. Rief, H. Lehmann, M. Ludwig, C. Dornmair, V.T. Moy, and H.E. Gaub, Biosens. Bioelectron. BBIOE4 0956-5663 10, 895 (1995). 10.1016/0956-5663(95)99227-C
34. M. Rief, H. Clausen-Schaumann, and H.E. Gaub, Nat. Struct. Biol. 6, 346 (1999). NSBIEW 1072-8368 10.1038/7582
35. W.K. Olson and J.L. Sussman, J. Am. Chem. Soc. 104, 270 (1982). JACSAT 0002-7863 10.1021/ja00365a049
36. M. Daune, Molecular Biophysics. Structures in Motion (Oxford University Press, New York, 1999), pp. 42-48.
37. N. Foloppe and A.D. MacKerell, J. Phys. Chem. B 102, 6669 (1998). JPCBFK 1520-6106 10.1021/jp9818683
38. C.S.M. Olsthoorn, L.J. Bostelaar, J.H.V. Boom, and C. Altona, European Journal of Biochemistry EJBCAI 0014-2956 112, 95 (1980). 10.1111/j.1432-1033. 1980.tb04991.x
39. H. Lu and K. Schulten, Proteins: Struct., Funct., Genet. PSFGEY 0887-3585 35, 453 (1999). 10.1002/(SICI)1097-0134(19990601)35:4<453::AID- PROT9>3.0.CO;2-M
40. T.G. Dewey and D.H. Turner, Biochemistry BICHAW 0006-2960 18, 5757 (1979). 10.1021/bi00593a002
41. R. Luo, H.S.R. Gilson, M.J. Potter, and M.K. Gilson, Biophys. J. 80, 140 (2001). BIOJAU 0006-3495
42. K.J. Breslauer and J.M. Sturtevant, Biophys. Chem. 7, 205 (1977). BICIAZ 0301-4622 10.1016/0301-4622(77)87023-3