Relative flexibility of DNA and RNA: A molecular dynamics study

Journal of Molecular Biology

Volumn 343, Issue 3, 2004, Pages 627-638

  Noy, Agnes ^a   Pérez, Alberto ^a   Lankas, Filip ^b   Javier Luque, F ^c   Orozco, Modesto ^a,c  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b EPFL   (Switzerland)

^c UNIVERSITY OF BARCELONA   (Spain)

Author keywords

DNA; flexibility; molecular dynamics; RNA; similarity indexes

Indexed keywords

DNA; RNA;

AQUEOUS SOLUTION; ARTICLE; GENE STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; RIGIDITY; SIMULATION;

EID: 4744350893     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.07.048     Document Type: Article

References (47)

1. V.A. Bloomfield, I. Tinoco, J.E. Hearst, and D.M. Crothers Nucleic Acids: Structures, Properties, and Functions 2000 University Science Books Sausalito, Calif
2. M.J. Gait, and G.M. Blackburn Nucleic Acids in Chemistry and Biology 1990 IRL Press at Oxford University Press Oxford
3. W. Saenger Principles of Nucleic Acid Structure 1984 Springer New York
4. R. Soliva, F.J. Luque, C. Alhambra, and M. Orozco Role of sugar re-puckering in the transition of A and B forms of DNA in solution. A molecular dynamics study J. Biomol. Struct. Dynam. 17 1999 89 99
5. A. Sancar DNA excision repair Annu. Rev. Biochem. 65 1996 43 81
6. P.I. Pradeepkumar, N.V. Amirkhanov, and J. Chattopadhyaya Antisense oligonuclotides with oxetane-constrained cytidine enhance heteroduplex stability, and elicit satisfactory RNase H response as well as showing improved resistance to both exo and endonucleases Org. Biomol. Chem. 1 2003 81 92
7. B. Verbeure, E. Lescrinier, J. Wang, and P. Herdewijn RNase H mediated cleavage of RNA by cyclohexene nucleic acid (CeNA) Nucl. Acids Res. 29 2001 4941 4947
8. A. Fire, S. Xu, M.K. Montgomery, S.A. Kostas, S.E. Driver, and C.C. Mello Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 391 1998 806 811
9. S.M. Hammond, A.A. Caudy, and G.J. Hannon Post-transcriptional gene silencing by double-stranded RNA Nature Rev. Genet. 2 2001 110 119
10. P.J. Hagerman Flexibility of DNA Annu. Rev. Biophys. Biophys. Chem. 17 1988 265 286
11. P.J. Hagerman Flexibility of RNA Annu. Rev. Biophys. Biomol. Struct. 26 1997 139 156
12. G.J. Thomas Jr, J.M. Benevides, S.A. Overman, T. Ueda, K. Ushizawa, M. Saitoh, and M. Tsuboi Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations Biophys. J. 68 1995 1073 1088
13. T. Fujiwara, and H. Shindo Phosphorus-31 nuclear magnetic resonance of highly oriented DNA fibers. 2. Molecular motions in hydrated DNA Biochemistry 24 1985 896 902
14. H. Shindo, T. Fujiwara, H. Akutsu, U. Matsumoto, and Y. Kyogoku Phosphorus-31 nuclear magnetic resonance of highly oriented DNA fibers. 1. Static geometry of DNA double helices Biochemistry 24 1985 887 895
15. T.E. Cheatham, and P.A. Kollman Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes J. Am. Chem. Soc. 119 1997 4805 4825
16. R.E. Dickerson, D.S. Goodsell, and S. Neidle "...the tyranny of the lattice..." Proc. Natl Acad. Sci. USA 91 1994 3579 3583
17. A. Lipanov, M.L. Kopka, M. Kaczor-Grzeskowiak, J. Quintana, and R.E. Dickerson Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA Biochemistry 32 1993 1373 1389
18. S. Portmann, N. Usman, and M. Egli The crystal structure of r(CCCCGGGG) in two distinct lattices Biochemistry 34 1995 7569 7575
19. Z. Shakked, G. Guerstein-Guzikevich, M. Eisenstein, F. Frolow, and D. Rabinovich The conformation of the DNA double helix in the crystal is dependent on its environment Nature 342 1989 456 460
20. Perez, A., Noy, A., Lankas, F., Luque, F. J. & Orozco, M. (2004). The relative flexibiliy of DNA and RNA a database analysis. Nucl. Acid Res. In the press.
21. P. Auffinger, and E. Westhof Water and ion binding around RNA and DNA (C,G) oligomers J. Mol. Biol. 300 2000 1113 1131
22. P. Auffinger, and E. Westhof Water and ion binding around r(UpA)12 and d(TpA)12 oligomers - comparison with RNA and DNA (CpG)12 duplexes J. Mol. Biol. 305 2001 1057 1072
23. Y. Pan, and A.D. MacKerell Jr Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening Nucl. Acids Res. 31 2003 7131 7140
24. T.E. Cheatham, P. Cieplak, and P.A. Kollman A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dynam. 16 1999 845 862
25. M. Orozco, A. Perez, A. Noy, and F.J. Luque Theoretical methods for the simulation of nucleic acids Chem. Soc. Rev. 32 2003 350 364
26. S. Arnott, P.J. Bond, E. Selsing, and P.J. Smith Models of triple-stranded polynucleotides with optimised stereochemistry Nucl. Acids Res. 3 1976 2459 2470
27. M.J. Packer, and C.A. Hunter Sequence-dependent DNA structure: the role of the sugar-phosphate backbone J. Mol. Biol. 280 1998 407 420
28. S.A. Harris, E. Gavathiotis, M.S. Searle, M. Orozco, and C.A. Laughton Cooperativity in drug-DNA recognition: a molecular dynamics study J. Am. Chem. Soc. 123 2001 12658 12663
29. F. Lankas, J. Sponer, P. Hobza, and J. Langowski Sequence-dependent elastic properties of DNA J. Mol. Biol. 299 2000 695 709
30. X.J. Lu, Z. Shakked, and W.K. Olson A-form conformational motifs in ligand-bound DNA structures J. Mol. Biol. 300 2000 819 840
31. G.C. Shields, C.A. Laughton, and M. Orozco Molecular dynamics simulations of the d(T center dot A center dot T) triple helix J. Am. Chem. Soc. 119 1997 7463 7469
32. G.C. Shields, C.A. Laughton, and M. Orozco Molecular dynamics simulation of a PNA center dot DNA center dot PNA triple helix in aqueous solution J. Am. Chem. Soc. 120 1998 5895 5904
33. T. Darden, D. York, and L. Pedersen Particle Mesh Ewald - an N.Log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
34. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical-integration of cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes J. Comput. Phys. 23 1977 327 341
35. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, and D.M. Ferguson A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules J. Am. Chem. Soc. 117 1995 5179 5197
36. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
37. J.L. Gelpi, S.G. Kalko, X. Barril, J. Cirera, X. de La Cruz, F.J. Luque, and M. Orozco Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins Proteins: Struct. Funct. Genet. 45 2001 428 437
38. M. Orozco, and F.J. Luque Theoretical methods for the description of the solvent effect in biomolecular systems Chem. Rev. 100 2000 4187 4226
39. E.C. Sherer, S.A. Harris, R. Soliva, H. Orozco, and C.A. Laughton Molecular dynamics studies of DNA A-tract structure and flexibility J. Am. Chem. Soc. 121 1999 5981 5991
40. S.T. Wlodek, T.W. Clark, L.R. Scott, and J.A. McCammon Molecular dynamics of acetylcholinesterase dimer complexed with tacrine J. Am. Chem. Soc. 119 1997 9513 9522
41. E. Cubero, N.G.A. Abrescia, J.A. Subirana, F.J. Luque, and M. Orozco Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex J. Am. Chem. Soc. 125 2003 14603 14612
42. M. Rueda, S.G. Kalko, F.J. Luque, and M. Orozco The structure and dynamics of DNA in the gas phase J. Am. Chem. Soc. 125 2003 8007 8014
43. J. Schlitter Estimation of absolute and relative entropies of macromolecules using the covariance-matrix Chem. Phys. Letters 215 1993 617 621
44. I. Andricioaei, and M. Karplus On the calculation of entropy from covariance matrices of the atomic fluctuations J. Chem. Phys. 115 2001 6289 6292
45. F. Lankas, J. Sponer, J. Langowski, and T.E. Cheatham DNA basepair step deformability inferred from molecular dynamics simulations Biophys. J. 85 2003 2872 2883
46. A. Matsumoto, and W.K. Olson Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level Biophys. J. 83 2002 22 41
47. W.K. Olson, A.A. Gorin, X.J. Lu, L.M. Hock, and V.B. Zhurkin DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl Acad. Sci. USA 95 1998 11163 11168