The flexibility of locally melted DNA

Nucleic Acids Research

Volumn 37, Issue 14, 2009, Pages 4580-4586

  Forties, Robert A ^a   Bundschuh, Ralf ^a   Poirier, Michael G ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; SINGLE STRANDED DNA;

ARTICLE; CYCLIZATION; DNA DENATURATION; DNA SEQUENCE; DNA STRUCTURE; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROBABILITY; TEMPERATURE DEPENDENCE; THEORY;

DNA; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; TEMPERATURE;

EID: 69049100084     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp442     Document Type: Article

References (37)

1. Adhya,S. (1989) Multipartite genetic control elements - communication by DNA loop. Annu. Rev. Genet., 23, 227-250.
2. Moslaluk,C. and Bastia,D. (1987) DNA bending is induced in an enhancer by the DNA-binding domain of the bovine papillomavirus E2 protein. Proc. Natl Acad. Sci. USA, 85, 1826-1830.
3. Horikoshi,M., Bertuccioli,C., Takada,R., Wang,J., Yamamoto,T. and Roeder,R.G. (1992) Transcription factor TFIID induces DNA bending upon binding to the TATA element. Proc. Natl Acad. Sci. USA, 89, 1060-1064.
4. Rees,W., Keller,R., Vesenka,J., Yang,G. and Bustamante,C. (1987) Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science, 260, 1646-1649.
5. Nelson,D.L. and Cox,M.M. (2005) In Freeman,W.H. (ed.), Principles of Biochemistry, New York.
6. Shore,D. and Baldwin,R.L. (1983) Energetics of DNA twisting. J. Mol. Biol., 170, 957-981.
7. Vologodskaia,M. and Vologodskii,A. (2002) Contribution of the intrinsic curvature to measured DNA persistence length. J. Mol. Biol., 317, 205-213.
8. Du,Q., Smith,C., Shiffeldrim,N., Vologodskaia,M. and Vologodskii,A. (2005) Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl Acad. Sci. USA, 102, 5397-5402.
9. Bustamante,C., Marko,J.F., Siggia,E.D. and Smith,S. (1994) Entropic elasticity of lambda-phage DNA. Science, 265, 1599-1600.
10. Wang,M.D., Yin,H., Landick,R., Gelles,J. and Block,S.M. (1997) Stretching DNA with optical tweezers. Biophys. J., 72, 1335-1346.
11. Hansma,H.G., Revenko,I., Kim,K. and Laney,D.E. (1996) Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. Nucleic Acids Res., 24, 713-720.
12. Hansma,H.G., Kim,K.J., Laney,D.E., Garcia,R.A., Argaman,M., Allen,M.H. and Parsons,S.M. (1997) Properties of biomolecules measured from atomic force microscope images: A review. J. Struct. Biol., 119, 99-108.
13. Hagerman,P.J. (1988) Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem., 17, 265-286.
14. Cloutier,T.E. and Widom,J. (2004) Spontaneous sharp bending of double-stranded DNA. Mol. Cell, 14, 355.
15. Cloutier,T.E. and Widom,J. (2005) DNA twisting flexibility and the formation of sharply looped protein-DNA complexes. Proc. Natl Acad. Sci. USA, 102, 3645-3650.
16. Yuan,C.L., Chen,H.M., Lou,X.W. and Archer,L.A. (2008) DNA bending stiffness on small length scales. Phys. Rev. Lett., 100, 18102.
17. Shroff,H., Sivak,D., Siegel,J.J., McEvoy,A.L., Siu,M., Spakowitz,A., Geissler,P.L. and Liphardt,J. (2008) Optical measurement of mechanical forces inside short DNA loops. Biophys. J., 94, 2179-2186.
18. Wiggins,P.A., Van der Heijden,T., Moreno-Herrero,F., Spakowitz,A., Phillips,R., Widom,J., Dekker,C. and Nelson,P.C. (2006) High flexibility of DNA on short length scales probed by atomic force microscopy. Nat. Nanotechnol., 1, 137-141.
19. Chen,H., Liu,Y., Zhou,Z., Hu,L., Ou-Yang,Z. and Yan,J. (2009) Temperature dependence of circular DNA topological states. Phys. Rev. E, 79, 41926.
20. Chen,H. and Yan,J. (2008) Effects of kink and flexible hinge defects on mechanical responses of short double-stranded DNA molecules. Phys. Rev. E, 77, 41907.
21. Du,Q., Kotlyar,A. and Vologodskii,A. (2008) Kinking the double helix by bending deformation. Nucleic Acids Res., 36, 1120-1128.
22. Wiggins,P.A. and Nelson,P.C. (2006) Generalized theory of semi-flexible polymers. Phys. Rev. E, 73, 31906.
23. Yan,J. and Marko,J.F. (2004) Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett., 93 108108.
24. Yan,J., Kawamura,R. and Marko,J.F. (2005) Statistics of loop formation along double helix DNAs. Phys. Rev. E, 71, 61905.
25. SantaLucia,J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
26. Mathews,D.H., Disney,M.D., Childs,J.L., Schroeder,S.J., Zuker,M. and Turner,D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
27. Isaacs,R.J. and Spielmann,H.P. (2004) Insight into G-T mismatch recognition using molecular dynamics with time-averaged restraints derived from NMR spectroscopy. J. Am. Chem. Soc., 126, 583-590.
28. Kahn,J.D., Yun,E. and Crothers,D.M. (1994) Detection of localized DNA flexibility. Nature, 368, 163-166.
29. Krueger,A., Protozanova,E. and Frank-Kamenetskii,M.D. (2006) Sequence-dependent basepair opening in DNA double helix. Biophys. J. 90, 3091-3099.
30. Coleman,B.D., Olson,W.K. and Swigon,D. (2003) Theory of sequence-dependent DNA elasticity. J. Chem. Phys, 118, 7127-7140.
31. Becker,N.B., Wolff,L. and Everaers,R. (2006) Indirect readout: Detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials. Nucleic Acids Res., 34 5638-5649.
32. Gaillard,C. and Strauss,F. (1990) Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Res., 18, 378.
33. Rouzina,I. and Bloomfield,V.A. (1998) DNA bending by small, mobile multivalent cations. Biophys. J., 74, 3152-3164.
34. Duguet,M. (1993) The helical repeat of DNA at high temperature. Nucleic Acids Res., 21, 463-468.
35. Achter,E.K. and Felsenfeld,G. (1971) ssDNA persistence length. Biopolymers, 10, 1625-1634.
36. Mazurek,A., Johnson,C.N., Germann,M.W. and Fishel,R. (2009) Sequence context effect for hMSH2-hMSH6 mismatch-dependent activation. Proc. Natl Acad. Sci. USA, 106, 4177-4182.
37. Lowary,P.T. and Widom,J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol., 276, 19-42.