High pressure effects on conformation of homo- and heteroduplexes of nucleic acids

Biochimie

Volumn 78, Issue 10, 1996, Pages 862-867

  Krzyzaniak, A ^a   Furste J P ^b   Erdmann, V A ^c   Salanski, P ^c   Jurczak, J ^c   Barciszewski, J ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c INSTITUTE OF ORGANIC CHEMISTRY   (Poland)

Author keywords

Home and heteroduplexes; Nucleic acids; Oligonucleotides

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; DOUBLE STRANDED DNA; DOUBLE STRANDED RNA;

ARTICLE; CIRCULAR DICHROISM; CONFORMATION; CONFORMATIONAL TRANSITION; DNA RNA HYBRIDIZATION; HYPERBARISM; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; RNA RNA HYBRIDIZATION;

EID: 0030481196     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0300-9084(97)84339-8     Document Type: Article

References (34)

1. 1 Hall K, McLaughlin LW (1991) Thermodynamic and structural properties of pentamer DNA:DNA, RNA:RNA and DNA:RNA duplexes of identical sequence. Biochemistry 30, 10606-10613
2. 2 Leslie AGW, Arnott S, Chandrasekaran R, Ratliff RL (1980) Polymorphism of DNA double helices. J Mol Biol 143, 49-72
3. 3 Drew H, Takano T, Tanaka S, Itakura K, Dickerson RE (1980) High salt d(CpGpCpG), a left handed Z-DNA double helix. Nature 286, 567-573
4. 4 Pohl F, Jovin TM (1972) Salt induced cooperative conformational change of synthetic DNA. Equilibrium and kinetic studies with poly(dG-dC). J Mol Biol 67, 375-396
5. 5 Hall K, Cruz PC, van de Sande J, Jovin TM, Tinoco IJr (1984) Z-RNA - a left handed RNA double helix. Nature 311, 584-586
6. 6 Martin FH, Tinoco IJr (1980) DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exeptionally unstable and may facilitate termination of transcription. Nucleic Acids Res 8, 2295-2299
7. 7 Ebel S, Brown T, Lane AN (1994) Thermodynamic stability and solution conformation of tandem G (A mismatches in RNA and RNA:DNA hybrid duplexes. Eur J Biochem 220, 703-715
8. 8 Ratmayer L, Vinayah R, Zhong YY, Zon G, Wilson WD (1994) Sequence specific thermodynamic and structural properties for DNA:RNA duplexes. Biochemistry 33, 5298-5304
9. 9 Lane AN, Ebel S, Brown T (1993) NMR assignments and solution conformation of the DNA:RNA hybrid duplex d(GTGAACTT) (r(AAGUUCAC). Eur J Biochem 215, 297-306
10. 10 Salazar M, Champoux JJ, Reid BR (1993) Sugar conformations at hybrid duplex junctions in HIV-1 and Okazaki fragments. Biochemistry 32, 739-744
11. 11 Fedoroff OYu, Salazar M, Reid BR (1993) Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA. J Mol Biol 233, 509-523
12. 12 Sanghani SR, Lavery R (1994) Theoretical studies of DNA-RNA hybrid conformations. Nucleic Acids Res 22, 1444-1449
13. 13 Holbrook SR, Cheong C, Tinoco IJr, Kim SH (1991) Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 353, 579-581
14. 14 Krzyzaniak A, Salanski P, Jurczak J, Barciszewski J (1991) B-Z DNA reversible conformational changes effected by high pressure. FEBS Lett 279, 1-4
15. 15 Krzyzaniak A, Fürste JP, Bald R, Salanski P, Jurczak J, Erdmann VA, Barciszewski J (1994) A-Z RNA conformational changes effected by high pressure. Int J Biol Macromol 16, 159-162
16. 16 Jurczak J (1979) Stereochemistry of Diels-Alder reactions at high pressure. II. Influence of high pressure on asymetric induction in condensation of (-)-di-(R) methyl fumarate with butadiene and isoprene. Bull Chem Soc Jpn 52, 3438-3442
17. 10. Proc Natl Acad Sci USA 89, 9242-9246
18. 18 Fairall L, Martin S, Rhodes D (1989) The DNA binding site of the Xenopus transcription factor IIIA has non-B-form structure. EMBO J 8, 1809-1817
19. 19 Vorlickova M, Kypr J, Jovin TM (1988) Salt induced isomerization of synthetic RNA poly[r (AU)]. Biopolymers 27, 351-354
20. 20 Pohl FM, Jovin TM (1972) Salt induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC). J Mol Biol 67, 375-396
21. 21 Saenger W, Hunter WN, Kennard O (1986) DNA conformation is determined by economics in the hydration of phosphate groups. Nature 324, 385-388
22. 22 Mellema J-R, Haasnoot CAG, van der Marel GA, Wille G, van Boeckel CAA, van Boom JH, Altona C (1983) Proton NMR studies on the covalently linked RNA:DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect. Nucleic Acids Res 11, 5717-5738
23. 23 Reid DG, Salisbury SA, Brown T, Williams D, Vasseur J-J, Rayner RB, Imbach JL (1983) Use of the interproton nuclear Overhauser effects to assign the nuclear magnetic resonance spectra of oligonucleotide and hybrid duplexes in aqueous solutions. Eur J Biochem 135, 307-314
24. 24 Chou S-H, Flynn P, Reid B (1989) High resolution NMR study of a synthetic DNA-RNA hybrid dodecamer containing the consensus Pribnov promoter sequence d(CGTTATAATGCG)r(CGCAUUAUAACG). Biochemistry 28, 2435-2443
25. 25 Zimmerman SB, Pheiffer BH (1981) A RNA-DNA hybrid that can adopt two conformations; An X-ray diffraction study of poly(rA)poly(dT) in concentrated solutions or in fibers. Proc Natl Acad Sci USA 78, 78-82
26. 26 Kim K, Jhon MS (1979) Theoretical study of hydration of RNA. Biochim Biophys Acta 565, 131-147
27. 27 Gray DM, Ratliff RL (1975) Circular dichroism spectra of poly[d (AC)r (GT)], poly[r(AC)r(GU)] and hybrids poly[d(AC)r (GU)] and poly[r(AC)d(GT)] in the presence of ethanol. Biopolymers 14, 487-498
28. 28 Poncin M, Hartmann B, Lavery R (1992) Conformational sub-states in B-DNA. J Mol Biol 226, 775-794
29. 29 Chalikian TV, Sarvazyan AP, Plum E, Breslauer KJ (1994) Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of syntetic and natural DNA duplexes at 25°C. Biochemistry 33, 2394-2401
30. 30 Berman HM (1994) Hydration of DNA: take 2. Curr Opin Struct Biol 4, 345-350
31. 31 Premilat S, Albiser G (1995) Temperature effects on hydration and form transitions of DNA. CR Acad Sci Paris 318, 553-557
32. 32 Benson SW, Siebert ED (1992) A simple two structure model for liquid water J Am Chem Soc 114, 4269-4276
33. 33 Kitchen DB, Reed LH, Levy RM (1992) Molecular dynamics simulation of solvated protein at high pressure. Biochemistry 31, 10083-10093
34. 34 Timsit Y, Moras D (1994) DNA self-fitting: the double helix directs the geometry of its supramolecular assembly. EMBO J 13, 2737-2746