Parallel DNA double helices incorporating isoG or m 5isoC bases studied by FTIR, CD and molecular modeling

Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy

Volumn 61, Issue 4, 2005, Pages 579-587

  Geinguenaud, F ^a   Mondragon Sanchez, J A ^a   Liquier, J ^a   Shchyolkina, A K ^b   Klement, R ^c   Arndt Jovin, D J ^c   Jovin, T M ^c   Taillandier, E ^a  

^a UNIVERSITÉ PARIS 13   (France)

^b ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^c MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

CD; FTIR; Isoguanine; m 5Isocytosine; Modeling; Parallel DNA

Indexed keywords

ISOGUANINE; M5ISOCYTOSINE; MOLECULAR MODELING; PARALLEL-DNA;

ABSORPTION; CONCENTRATION (PROCESS); DNA; FOURIER TRANSFORM INFRARED SPECTROSCOPY; FREE ENERGY; GEOMETRY; HYDROGEN BONDS; NUCLEIC ACIDS; ULTRAVIOLET RADIATION;

MOLECULAR ORIENTATION;

CARBOHYDRATE; CYTOSINE; DEOXYRIBOSE; DNA; DRUG DERIVATIVE; GUANINE; ISOCYTOSINE; ISOGUANINE; THYMINE;

ARTICLE; BASE PAIRING; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; CONFORMATION; DNA BASE COMPOSITION; DNA DENATURATION; HYDROGEN BOND; INFRARED SPECTROSCOPY; METHODOLOGY; SPECTROPHOTOMETRY;

BASE COMPOSITION; BASE PAIRING; CARBOHYDRATES; CIRCULAR DICHROISM; CYTOSINE; DEOXYRIBOSE; DNA; GUANINE; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; SPECTROPHOTOMETRY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; THYMINE;

EID: 11344257178     PISSN: 13861425     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.saa.2004.05.037     Document Type: Article

References (56)

1. S. Arnott S. Neidle Oxford Handbook of Nucleic Acid Structure 1999 Oxford Press 1 38
2. R.E. Dickerson, H.R. Drew, B.N. Conner, R.M. Wing, A.V. Fratini, and M.L. Kopka Science 216 1982 475 485
3. A.H-J. Wang, G.J. Quigley, F.J. Kolpak, J.L. Crawford, J.H. van Boom, G. Van der Marel, and A. Rich Nature (London) 282 1979 680 686
4. O. Kennard, and W. Hunter Q. Rev. Biophys. 22 1989 327 379
5. D. Sen, and W. Gilbert Methods Enzymol. 211 1992 191 199
6. Y. Wang, and D.J. Patel J. Mol. Biol. 251 1995 76 79
7. F.W. Smith, and J. Feigon Nature 356 1992 164 168
8. J.A. Kelly, J. Feigon, and T.O. Yeates J. Mol. Biol. 256 1996 417 422
9. V.M. Marathias, and P.H. Bolton Nucleic Acids Res. 28 9 2000 1969 1977
10. K. Gehring, J.L. Leroy, and M. Guéron Nature 363 1993 561 565
11. I. Radhakrishnan, and D.J. Patel Biochemistry 33 1994 11405 11416
12. V.N. Soyfer, and V.N. Potaman Triple Helical Nucleic Acids 1996 Springer-Verlag New York
13. E. Wang, and J. Feigon S. Neidle Oxford Handbook of Nucleic Acid Structure 1999 Oxford Press 355 388
14. K. Rippe, and T.M. Jovin Methods Enzymol. 11 1992 199 220
15. M.W. Germann, N. Zhou, J.H. Van de Sande, and H.J. Vogel Methods Enzymol. 261 1995 207 225
16. S.C. Ekker, and J.D. Larson Genesis 30 2001 89 93
17. J. Kurreck Eur. J. Biochem. 270 2003 1628 1644
18. B.P. Monia, J.F. Johnston, T. Geiger, M. Muller, and D. Fabbro Nat. Med. 2 1996 668 675
19. H. Gousset, J. Liquier, E. Taillandier, Y.S. Sanghvi, and D. Peoc'h J. Biomol. Struct. Dyn. 15 1998 931 936
20. M. Egli, and S. Gryaznov Cell Mol. Life Sci. 57 2000 1440 1456
21. C. Switzer, and J.C. Chaput Methods 23 2001 141 148
22. M.W. Germann, B.W. Kalisch, and J.H. van de Sande Biochemistry 27 1988 8302 8306
23. M.W. Germann, B.W. Kalisch, R.T. Pon, and J.H. van de Sande Biochemistry 29 1990 9426 9432
24. C. Otto, G.A. Thomas, K. Rippe, T.M. Jovin, and W.L. Peticolas Biochemistry 30 1991 3062 3069
25. H. Fritzsche, A. Akhebat, E. Taillandier, K. Rippe, and T.M. Jovin Nucleic Acids Res. 21 1993 5085 5091
26. K. Rippe, N.B. Ramsing, R. Klement, and T.M. Jovin J. Biomol. Struct. Dyn. 7 1990 1199 1209
27. S. Mohammadi, R. Klement, A.K. Shchyolkina, J. Liquier, T.M. Jovin, and E. Taillandier Biochemistry 37 1998 16529 16537
28. A.K. Shchyolkina, O.F. Borisova, A. Livshits, G.E. Pozmogova, B.K. Chernov, R. Klement, and T.M. Jovin Biochemistry 39 2000 10034 10044
29. K. Rippe, V. Kuryavyi, E. Westhof, and T.M. Jovin D.M. Lilley H. Heuman D. Suck Advances in Life Sciences 1992 Birkhauser Verlag Basel 81 107
30. H. Sugiyama, S. Ikeda, and I. Saito J. Am. Chem. Soc. 118 1996 9994 9995
31. C. Roberts, R. Bandaru, and C. Switzer J. Am. Chem. Soc. 119 1997 4640 4649
32. F. Seela, and C. Wei Helv. Chim. Acta 80 1997 73 85
33. F. Seela, C. Wei, A. Melenewski, and P. Leonard Nucleic Acids Symp. Ser. 37 1997 149 150
34. X.L. Yang, H. Sugiyama, S. Ikeda, I. Saito, and A.H.-J. Wang Biophys. J. 75 1998 1163 1171
35. F. Seela, Y. He, and C. Wei Tetrahedron 55 1999 9481 9500
36. A.K. Shchyolkina, O.F. Borisova, and T.M. Jovin Nucleosides Nucleotides 18 1999 1555 1562
37. E. Taillandier, and J. Liquier Methods Enzymol. 211 1992 307 355
38. E. Taillandier, and J. Liquier J.M. Chalmers P.R. Griffith Handbook of Vibrational Spectroscopy vol. 5 2002 John Wiley & sons Chichester (pp. 3465-3480)
39. V.I. Ivanov, L.E. Minchenkova, A.K. Shchyolkina, and A.I. Poletayev Biopolymers 12 1973 89 110
40. G.G. Malenkov, L. Minchenkova, E. Minyat, A.K. Shchyolkina, and V.I. Ivanov FEBS Lett. 51 1975 38 42
41. C.S. Tung, and E.S. Carter CABIOS 10 1994 427 433
42. D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheatham III, W.S. Ross, C.L. Simmerling, T.A. Darden, K.M. Merz, R.V. Stanton, A.L. Cheng, J.J. Vincent, M. Crowley, D.M. Ferguson, R.J. Radmer, G.L. Seibel, U.C. Singh, P.K. Weiner, and P.A. Kollman AMBER 5 1997 University of California San Francisco
43. M.J. Frisch, G.W. Trucks, H.B. Schlegel, P.M.W. Gill, G. Johnson, M.A. Robb, J.R. Cheeseman, T.A. Keith, G.A. Petersson, J.A. Montgomery, K. Raghavacheri, M.A. Al-Laham, V.G. Zakrzewski, J.V. Ortiz, J.B. Foresman, J. Cioslowski, B.B. Stefanov, A. Nanayakkara, M. Challacombe, C.Y. Peng, P.Y. Ayala, W. Chen, M.W. Wong, J.L. Andres, E.S. Replogle, R. Gomperts, R.L. Martin, D.J. Fox, J.S. Binkley, D.J. Defrees, J. Baker, J.P. Stewart, M. Head-Gordon, C. Gonzalez, and J.A. Pople Gaussian 94 1995 Gaussian, Inc. Pittsburgh, PA
44. R. Lavery, H. Sklenar, CURVES 5.1 Helical analysis of irregular DNA structures, http://www.ibpc.fr/UPR9080/Curindex.html.
45. W. Humphrey, A. Dalke, and K. Schulten VMD - visual molecular dynamics J. Mol. Graph. 14 1996 33 38
46. M. Tsuboi, S. Takahashi, and I. Harada G. Duchesne Physicochemical Properties of Nucleic Acids 1973 Academic Press London 91 145
47. W. Krzyzosiak, M. Jaskolski, H. Sierzputowska-Gracz, and M. Wiewiorowski Nucleic Acids Res. 10 1982 2741
48. H.T. Miles, and J. Frazier Biochem. Biophys. Res. Commun. 49 1972 199 204
49. E. Liquier, and Taillandier H.H. Mantsch D. Chapman Infrared Spectroscopy of Biomolecules 1996 John Wiley & Sons Chichester 131 158
50. J. Pilet, and J. Brahms Biopolymers 12 1973 387 403
51. W. Pohle, and H. Fritzsche Nucleic Acids Res. 8 1980 2527 2535
52. J. Liquier, A. Akhebat, E. Taillandier, F. Ceolin, T. Huynh-Dinh, and J. Igolen Spectrochim. Acta 47A 1991 177 186
53. L.E. Minchenkova, A.K. Shchyolkina, B.K. Chernov, and V.I. Ivanov J. Biomol. Struct. Dyn. 4 1986 463 476
54. M.Y. Tolstorukov, V.I. Ivanov, G.G. Malenkov, R. Jernigan, and V.B. Zhurkin Biophys. J. 81 2001 3409 3421
55. A.K. Shchyolkina, L.E. Minchenkova, V.I. Ivanov, V.V. Butkus, and A.A. Ianulaitis Mol. Biol. (Mosk) 22 1988 1562 1570
56. E. Taillandier, J. Liquier, and J.A. Taboury R.J.H. Clark R.E. Hester Advances in Infrared and Raman Spectroscopy vol. 12 1985 Wiley Heyden (pp. 65-114)