Sequence dependence of DNA bending rigidity

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 35, 2010, Pages 15421-15426

  Geggier, Stephanie ^a   Vologodskii, Alexander ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

DNA elasticity; DNA persistence length

Indexed keywords

CURVED DNA; DINUCLEOTIDE; DNA FRAGMENT; REPETITIVE DNA;

ARTICLE; CYCLIZATION; DNA CONFORMATION; DNA PROTEIN COMPLEX; DNA SEQUENCE; PRIORITY JOURNAL; PROTEIN INTERACTION;

ALGORITHMS; BASE SEQUENCE; DNA; DNA, CIRCULAR; ELECTROPHORESIS, AGAR GEL; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES;

EID: 77957255973     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1004809107     Document Type: Article

References (49)

1. Hagerman PJ (1988) Flexibility of DNA. Annu Rev Biophys Bio 17:265-286.
2. Taylor WH, Hagerman PJ (1990) Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. J Mol Biol 212:363-376. (Pubitemid 20130734)
3. Vologodskaia M, Vologodskii A (2002) Contribution of the intrinsic curvature to measured DNA persistence length. J Mol Biol 317:205-213.
4. Widom J (2001) Role of DNA sequence in nucleosome stability and dynamics. Q Rev Biophys 34:269-324.
5. Travers AA (2004) The structural basis of DNA flexibility. Philos Trans Roy Soc A 362:1423-1438.
6. Okonogi TM, Alley SC, Reese AW, Hopkins PB, Robinson BH (2002) Sequence-dependent dynamics of duplex DNA: The applicability of a dinucleotide model. Biophys J 83:3446-3459.
7. Lankas F (2006) Sequence-dependent harmonic deformability of nucleic acids inferred from atomistic molecular dynamics. Computational Studies of RNA and DNA, eds J Sponer and F Lankas (Springer, Dordrecht, The Netherlands), pp 559-577.
8. Anselmi C, Bocchinfuso G, De Santis P, Savino M, Scipioni A (2000) A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys J 79:601-613.
9. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 95:11163-11168.
10. Balasubramanian S, Xu F, Olson WK (2009) DNA sequence-directed organization of chromatin: Structure-based computational analysis of nucleosome-binding sequences. Biophys J 96:2245-2260.
11. Shore D, Langowski J, Baldwin RL (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci USA 78:4833-4837. (Pubitemid 12225575)
12. Shore D, Baldwin RL (1983) Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol 170:957-981.
13. Trifonov EN, Tan RKZ, Harvey SC (1988) Static persistence length of DNA. DNA Bending and Curvature, eds WK Olson, MH Sarma, RH Sarma, and M Sundaralingam (Adenine, New York), pp 243-253.
14. Schellman JA, Harvey SC (1995) Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys Chem 55:95-114.
15. Bensimon D, Dohmi D, Mezard M (1998) Stretching a heteropolymer. Europhys Lett 42:97-102.
16. Koo HS, Wu HM, Crothers DM (1986) DNA bending at adenine-thymine tracts. Nature 320:501-506.
17. Hagerman PJ (1986) Sequence-directed curvature of DNA. Nature 321:449-450.
18. Crothers DM, Drak J, Kahn JD, Levene SD (1992) DNA bending, flexibility, and helical repeat by cyclization kinetics. Method Enzymol 212:3-29.
19. MacDonald D, Herbert K, Zhang X, Polgruto T, Lu P (2001) Solution structure of an A-tract DNA bend. J Mol Biol 306:1081-1098.
20. Brukner I, Susic S, Dlakic M, Savic A, Pongor S (1994) Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J Mol Biol 236:26-32. (Pubitemid 24148944)
21. Landau L, Lifshitz E (1980) Statistical Physics (Elsevier, Oxford), pp 396-400.
22. Schellman JA (1974) Flexibility of DNA. Biopolymers 13:217-226.
23. Shimada J, Yamakawa H (1984) Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17:689-698.
24. Vologodskii A (2006) Simulation of equilibrium and dynamic properties of large DNA molecules. Computational Studies of DNA and RNA, eds F Lankas and J Sponer (Springer, Dordrecht, The Netherlands), pp 579-604.
25. Zhurkin VB, Lysov YP, Ivanov VI (1979) Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res 6:1081-1096.
26. Zhang Y, Crothers DM (2003) Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophys J 84:136-153.
27. Gray DM, Tinoco I (1970) A new approach to the study of sequence-dependent properties of polynucleotides. Biopolymers 9:223-244.
28. Goldstein RF, Benight AS (1992) How many numbers are required to specify sequence-dependent properties of polynucleotides? Biopolymers 32:1679-1693.
29. Jacobson H, Stockmayer WH (1950) Intramolecular reaction in polycondensation. I. Theory of linear systems. J Chem Phys 18:1600-1606.
30. Peck LJ, Wang JC (1981) Sequence dependence of the helical repeat of DNA in solution. Nature 292:375-378.
31. Strauss F, Gaillard C, Prunell A (1981) Helical periodicity of DNA, Poly(dA).poly(dT) and poly(dA-dT). poly(dA-dT) in solution. Eur J Biochem 118:215-222.
32. Alexeev DG, Lipanov AA, Skuratovskii IY (1987) Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove. Nature 325:821-823.
33. Vologodskii AV, Amirikyan BR, Lyubchenko YL, Frank-Kamenetskii MD (1984) Allowance for heterogeneous stacking in the DNA helix-coil transition theory. J Biomol Struct Dyn 2:131-148.
34. Licinio P, Guerra JC (2007) Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets. Biophys J 92:2000-2006.
35. SantaLucia J, Jr, Allawi HT, Seneviratne PA (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555-3562. (Pubitemid 26092574)
36. Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423:145-150.
37. Becker NA, Kahn JD, Maher LJ, 3rd (2005) Bacterial repression loops require enhanced DNA flexibility. J Mol Biol 349:716-730.
38. Swigon D, Coleman BD, Olson WK (2006) Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci USA 103:9879-9884.
39. Huo YX, et al. (2009) IHF-binding sites inhibit DNA loop formation and transcription initiation. Nucleic Acids Res 37:3878-3886.
40. Bolshoy A (1995) CC dinucleotides contribute to the bending of DNA in chromatin. Nat Struct Biol 2:446-448.
41. Lowary PT, 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.
42. Goulet I, Zivanovic Y, Prunell A (1987) Helical repeat of DNA in solution. The V curve method. Nucleic Acids Res 15:2803-2821.
43. Protozanova E, Yakovchuk P, Frank-Kamenetskii MD (2004) Stacked-unstacked equilibrium at the nick site of DNA. J Mol Biol 342:775-785.
44. Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 34:564-574. (Pubitemid 43240244)
45. El Hassan MA, Calladine CR (1997) Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Philos Trans Roy Soc A 355:43-100.
46. Du Q, Smith C, Shiffeldrim N, Vologodskaia M, Vologodskii A (2005) Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc Natl Acad Sci USA 102:5397-5402. (Pubitemid 40530269)
47. Dennis JE, Jr, Schnabel RT (1983) Numerical Methods for Unconstrained Optimization and Nonlinear Equations (Prentice Hall, Englewood Cliffs, NJ), pp 111-154.
48. Thastrom A, et al. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J Mol Biol 288:213-229.
49. Podtelezhnikov AA, Mao C, Seeman NC, Vologodskii AV (2000) Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophys J 79:2692-2704.