Helix-helix transitions in DNA: Fibre X-ray study of the particular cases poly(dG-dC) · poly(dG-dC) and poly(dA) · 2poly(dT)

European Biophysics Journal

Volumn 28, Issue 7, 1999, Pages 574-582

  Premilat, Samuel ^a   Albiser, Guy ^a  

^a NANCY UNIVERSITÉ   (France)

Author keywords

2poly(dT); B B* DNA structural transition; Poly(dA); Poly(dG dC); Right handed S DNA models; X ray fibre diffraction

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA HELIX; STRUCTURE ANALYSIS; X RAY DIFFRACTION;

DNA; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; POLYDEOXYRIBONUCLEOTIDES; X-RAY DIFFRACTION;

EID: 0032699641     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490050239     Document Type: Article

References (42)

1. Abouelkassimi A, Albiser G, Premilat S (1991) Conformational transitions and hydration of poly d(A-T) · poly d(A-T) in fibres. Eur Biophys J 20: 109-114
2. Albiser G, Premilat S (1992) B-Z conformational transition and hydration of poly(dC-dG) · poly(dC-dG) in fibres. Int J Biol Macromol 14: 161-165
3. Arnott S, Chandrasekaran R, Birdsall DL, Leslie AGW, Ratliff RL (1980) Left-handed DNA helices. Nature 283: 743-745
4. Arnott S, Selsing E (1974) Structure for polynucleotide complexes poly(dA) · poly(dT) and poly(dT) · poly(dA) · poly(dT). J Mol Biol 88: 509-521
5. 5dC) and poly (dG-dC) · poly(dG-dC) associated with the B-Z transition. Nature 293: 233-235
6. Cochran W, Crick FHC, Vand V (1952) The structure of synthetic polypeptides. I. The transforms of atoms on a helix. Acta Crystallogr 5: 581-586
7. Davies DR, Baldwin RL (1963) X-ray studies of two synthetic DNA copolymers. J Mol Biol 6: 251-255
8. Fraser RDB, MacRae TP, Suzuki E (1978) An improved method for calculating the contribution of solvent of the X-ray diffraction pattern of biological molecules. J Appl Crystallogr 11: 693-694
9. Fuller W (1959) Hydrogen bond lengths and angles observed in crystals. J Phys Chem 63: 1705-1717
10. Fuller W, Wilkins MHF, Wilson HR, Hamilton LD (1965) X-ray diffraction study of the A form. J Mol Biol 12: 60-80
11. Fuller W, Pigram WJ, Mahendrasingam A, Forsyth VT, Nave C, Greenall RJ (1984) X-ray diffraction studies of the polynucleotides poly d(A-T) · poly d(A-T) and poly d(G-C) · poly d(G-C). In: Biological systems structure and analysis: proceedings of the study weekend at Daresbury Laboratory. Science & Engineering Research Council, Daresbury, Warrington WA4 4AD, pp 106-108
12. Gelbin A, Schneider B, Clowney L, Hsieh SH, Olson WK, Berman HM (1996) Geometric parameters in nucleic acids: sugar and phosphate constituents. J Am Chem Soc 118: 519-529
13. Herrera JE, Chaires JB (1989) A premelting conformational transition in poly(dA) · poly(dT) coupled to daunomycin binding. Biochemistry 28: 1993-2000
14. Kan Y, Armitage B, Schuster GB (1997) Selective stabilization of triplex DNA by anthraquinone sulfonamide derivatives. Biochemistry 36: 1461-1466
15. Kennard O, Hunter WN (1989) Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies. Q Rev Biophys 22: 327-379
16. Klug A, Jack A, Viswamitra MA, Kennard O, Shakked Z, Steitz TA (1979) A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lacrepresor protein. J Mol Biol 131: 669-680
17. Lamiri A, Albiser G, Premilat S (1998) Polymorphism and disorder of poly(dA) · poly(dT) in fibers. Biochem Biophys Res Commun 253: 809-812
18. Langridge R, Wilson HR, Hooper CW, Wilkins MHF, Hamilton LD (1960a) The molecular configuration of deoxyrinucleic acid, I. X-ray diffraction study of a crystalline form of the lithium salt. J Mol Biol 2: 19 37
19. Langridge R, Marvin DA, Seeds WE, Wilson HR, Hooper CW, Wilkins MHF, Hamilton LD (1960b) The molecular configuration of deoxyrinucleic acid, II. Molecular models and their Fourier transforms. J Mol Biol 2: 38 64
20. Leslie AGW, Arnott S, Chandrasekaran R, Ratliff RL (1980) Polymorphism of DNA double helices. J Mol Biol 143: 49-72
21. Lomonossoff GP, Butler PJG, Klug A (1981) Sequence-dependent variation in the conformation of DNA. J Mol Biol 149: 745-760
22. Mahendrasingam A, Pigram WJ, Fuller W, Brahms J. Vergne J (1983) Conformational transitions in the synthetic polynucleotide poly(dG-dC) · poly(dG-dC) double-helix. J Mol Biol 168: 897-901
23. Mahendrasingam A, Denny RC, Forsyth VT, Greenall RJ, Pigram WJ, Papiz MZ, Fuller W (1990) Time-resolved X-ray fibre diffraction studies of the S-B conformational transition in the poly(dG-dC) · poly(dG-dC) double helix. Inst Phys Conf Ser 101: 225-236
24. Malinina L, Fernandez LG, Huynh-Dinh T, Subirana JA (1999) Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features. J Mol Biol 285: 1679-1690
25. Norden B, Kubista M, Kurucsev T (1992) Linear dichroism spectroscopy of nucleic acids. Q Rev Biophys 25: 51-170
26. 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
27. Park HS, Arnott S, Chandrasekaran R, Millane RP, Campagnari F (1987) Structure of the α-form of poly(dA) · poly(dT) and related polynucleotide duplexes. J Mol Biol 197: 513-523
28. Patel DJ, Canuel LL, Pohl FM (1979) Alternating B-DNA conformation for the oligo(dG-dC) duplex in high-salt solution. Proc Natl Acad Sci USA 76: 2508-2511
29. Patel DJ, Shapiro L, Hare D (1987) Nuclear magnetic resonance and distance geometry studies of DNA structures in solution. Annu Rev Biophys Chem 16: 423-454
30. Premilat S, Albiser G (1983) Conformations of A-DNA and B-DNA in agreement with fiber X-ray and infrared dichroism. Nucleic Acids Res 11: 92-104
31. Premilat S, Harmouchi M, Albiser G (1990) A method for the experimental study of DNA conformational transitions in fibers. Biophys Chem 35: 37-45
32. Premilat S, Albiser G (1997) X-ray fibre diffraction study of an elevated temperature structure of poly(dA) · poly(dT). J Mol Biol 274: 64-71
33. Saenger W (1984) Principles of nucleic acid structure. Springer, Berlin Heidelberg New York
34. Seeman NC, Rosenberg JM, Suddath FL, Kim JJP, Rich A (1976) RNA double-helical fragments at atomic resolution: 1. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate. J Mol Biol 104: 109-144
35. 31P-NMR of DNA fibers. Biophys J 73: 1539-1552
36. Sun JS, Helene C (1993) Oligonucleotide-directed triple-helix formation. Cur Opin Struct Biol 3: 345-356
37. Taillandier E, Liquier J (1992) Infrared spectroscopy of DNA. Methods Enzymol 211A: 307-335
38. Taylor R, Kennard O (1982) Comparison of X-ray and neutron diffraction results for the N - H ⋯ O=C hydrogen bond. Acta Crystallogr B39: 133-138
39. 5CGCGCGC). J Mol Biol 270: 247-258
40. Wahl MC, Rao ST, Sundaralingam M (1996) Crystal structure of the B-DNA hexamer d(CTCGAG): model for an A-to-B transition. Biophys J 70: 2857-2866
41. Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A (1979) Molecular structure of a left handed double helical DNA fragment at atomic resolution. Nature 282: 680-686
42. Wang AHJ, Quigley GJ, Kolpak FJ, van der Marel G, van Boom JH, Rich A (1981) Left-handed double helical DNA: variations in the backbone conformation. Science 211: 171-176