Conformational Effects of DNA Stretching

Molecular Biology

Volumn 37, Issue 2, 2003, Pages 240-249

  Mazur, J ^a,b   Jernigan, R L ^c,d   Sarai, A ^e  

^a SAIC FREDERICK INC   (United States)

^b NIH ^*  (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d IOWA STATE UNIVERSITY   (United States)

^e RIKEN TSUKUBA INSTITUTE   (Japan)

Author keywords

DNA flexibility; Propeller twist; Stress strain relation

Indexed keywords

DNA; DNA BASE;

ACCURACY; ARTICLE; BASE PAIRING; DNA BASE COMPOSITION; DNA CONFORMATION; DNA DETERMINATION; DNA HELIX; DNA STRAND; MOLECULAR STABILITY; PROTEIN PROTEIN INTERACTION; STATISTICAL SIGNIFICANCE; STRESS STRAIN RELATIONSHIP;

EID: 0037273125     PISSN: 00268933     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1023397622116     Document Type: Article

References (32)

1. Smith S.B., Finzi L., Bustamante C. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 258, 1122-1126.
2. Bensimon A., Simon A., Chiffaudel A., Croquette V., Heslot F., Bensimon D. 1994. Alignment and sensitive detection of DNA by a moving interface. Science. 265, 2096-2098.
3. Cluzel P., Lebrun A., Heller C., Lavery R., Vivoy J-L., Chatenay D., Caron F. 1996. DNA: an extensible molecule. Science. 271, 792-794.
4. Wang M.D., Ying H., Landick R., Gelles J., Block S.M. 1997. Stretching DNA with optical tweezers. Biophys. J. 72, 1335-1346.
5. Strick T.R., Croquette V., Bensimon D. 1998. Homologous pairing in stretched supercoiled DNA. Proc. Natl. Acad. Sci. USA. 95, 10579-10583.
6. Smith S.B., Cui Y., Bustamante C. 1996. Overstretching B-DNA: elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271, 795-799.
7. Egelman E.H., Yu X. 1989. The location of DNA in RecA-DNA helical filaments. Science. 245, 404-407.
8. Story R.M., Weber I.T., Steiz T.A. 1992. The structure of the E. coli. RecA protein monomer and polymer. Nature. 355, 318-325.
9. Egelman E.H. 2001. Does a stretched DNA structure dictate the helical geometry of RecA-like filaments? J. Mol. Biol. 309, 539-542.
10. Lebrun A., Lavery R. 1996. Modelling extreme stretching of DNA. Nucleic Acids Res. 24, 2260-2267.
11. Konrad M.W., Bolonick J.I. 1996. Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure. J. Am. Chem. Soc. 118, 10989-10994.
12. Kosikov K.M., Gorin A.A., Zhurkin V.B., Olson W.K. 1999. DNA stretching and compression: large-scale simulations of double helical structures. J. Mol. Biol. 289, 1301-1326.
13. MacKerell A.D. Jr., Lee G.U. 1999. Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads. Eur. Biophys J. 28, 415-426.
14. Olson W.K., Zhurkin V.B. 2000. Modeling DNA deformations. Curr. Opin. Struct. Biol. 10, 286-297.
15. Sarai A., Mazur J., Nussinov R., Jernigan R.L. 1988. Sequence dependence of DNA conformations: means and fluctuations. In Structure and Expressions. Eds Olson W.K., Sarma M.H., Sundaralingam M. N.-Y.: Adenine Press. 3, 213-222.
16. Sarai A., Mazur J., Nussinov R., Jernigan R.L. 1988. Origin of DNA helical structure and its sequence dependence. Biochemistry. 27, 8498-8502.
17. Mazur J., Sarai A., Jernigan R.L. 1989. Sequence dependence of the B-A conformational transition of DNA. Biopolymers. 28, 1223-1233.
18. Sarai A., Mazur J., Nussinov R., Jernigan R.L. 1989. Sequence dependence of DNA conformational flexibility. Biochemistry. 28, 7842-7849.
19. Mazur J., Jernigan R.L., Sarai A. 1996. Constructing optimal backbone segments for joining fixed DNA base Pairs. Biophys. J. 71, 1493-1506.
20. Sarai A., Jernigan R.L., Mazur J. 1996. Interdependence of conformational variables in double helical DNA. Biophys. J. 71, 1507-1517.
21. Goldstein H. Classical Mechanics. N.-Y.: Addison-Wesley Publishing Company, 1981.
22. Zhurkin V.B., Poltev V.I., Florent'ev V.I. 1981. Atom-atom potential functions for conformational calculations of nucleic acids. Mol. Biol. 14, 887-895.
23. Mazur J., Jernigan R.L. 1991. Distance-dependent dielectric constants and their application to double-helical DNA. Biopolymers. 31, 1615-1629.
24. Dickerson R.E., Drew H.R. 1981. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J. Mol. Biol. 149, 761-786.
25. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz Jr.K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. 1995. A second generation force field for the simulation of proteins and nucleic acids. J. Am. Chem. Soc. 117, 5179-5197.
26. Lebrun A., Shakked Z., Lavery R. 1997. Local DNA stretching mimics the distortion caused by the TATA box-binding protein. Proc. Natl. Acad. Sci. USA. 94, 2993-2998.
27. Drew H.R., Travers A.A. 1985. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186, 773-790.
28. Koudelka G.B., Harrison S.C., Ptashne M. 1987. Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature. 326, 886-888.
29. Hogan M.E., Austin R.H. 1987. Importance of DNA stiffness in protein-DNA binding specificity. Nature. 329, 263-266.
30. Goodman S.D., Nash H.A. 1989. Functional replacement of a protein-induced bend in a DNA recombination site. Nature. 368, 251-254.
31. Mishmar D., Rahat A., Scherer S.W., Nyakatura G., Hinzmann B., Kohwi Y., Mandel-Gutfroind Y., Lee J.R., Drescher B., Sas D.E., Margalit H., Platzer M., Weiss A., Tsui L.C., Rosenthal A., Kerem B. 1998. Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site. Proc. Natl. Acad. Sci. USA. 95, 8141-8146.
32. Pedersen A.G., Jensen L.J., Brunak S., Staerfeldt H.H., Ussery D.W. 2000. A DNA structural atlas for Escherichia coli. J. Mol. Biol. 299, 907-930.