Conformational polymorphism of d(A-G)n and related oligonucleotide sequences

Progress in Nucleic Acid Research and Molecular Biology

Volumn 75, Issue , 2003, Pages 321-347

  Dolinnaya, Nina G ^a,b   Fresco, Jacques R ^a  

^a PRINCETON UNIVERSITY   (United States)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOSIDE PHOSPHATE; OLIGONUCLEOTIDE;

BASE PAIRING; CHEMISTRY; CONFORMATION; GENETICS; PH; REVIEW; THERMODYNAMICS;

BASE PAIRING; DINUCLEOSIDE PHOSPHATES; HYDROGEN-ION CONCENTRATION; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; THERMODYNAMICS;

EID: 1542465940     PISSN: 00796603     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6603(03)75009-0     Document Type: Review

References (63)

1. R. D. Wells, D. A. Collier, J. C. Hanvey, M. Shimizu and F. Wohlrab, The chemistry and biology of unusual DNA structures adopted by oligopurine-oligopyrimidine sequences, FASEB J. 2, 2939-2949 (1988).
2. H. Manor, B. S. Rao and R. G. Martin, Abundance and degree of dispersion of genomic d(GA)n.d(TC)n sequences, J. Mol. Evol. 27, 96-101 (1988).
3. R. Kolluri, T. A. Torrey and A. J. Kinniburgh, A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif, Nucleic Acids Res. 20, 111-116 (1992).
4. n sequence repeats in DNA, Nucleic Acids Res. 21, 5221-5228 (1993).
5. K. Rippe, V. Fritsch, E. Westhof and T. M. Jovin, Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex, EMBO J. 11, 3777-3786 (1992).
6. n DNA sequences form antiparallel stranded homoduplexes stabilized by the formation of G A base pairs, EMBO J. 12, 4029-4038 (1993).
7. M. Vorličkova, I. Kejnovska, J. Kovanda and J. Kypr, Dimerization of the guanine-adenine repeat strands of DNA, Nucleic Acids Res. 27, 581-586 (1999).
8. 10, Proc. Natl. Acad. Sci. USA 89, 9242-9246 (1992).
9. 10, a single-stranded nucleic acid helix without paired or stacked bases, Biochemistry 32, 10263-10270 (1993).
10. n, Biochemistry 34, 14293-14299 (1995).
11. 10, a single-stranded helix without stacked or paired bases, Biochemistry 34, 14300-14303 (1995).
12. +) and DNA, Nucleic Acids Res. 25, 1100-1107 (1997).
13. M. C. Shiber, E. H. Braswell, H. Klump and J. R. Fresco, Duplex-tetraplex equilibrium between a hairpin and two interacting hairpins of d(A-G)10 at neutral pH, Nucleic Acids Res. 24, 5004-5012 (1996).
14. J. G. Nadeau and P. T. Gilham, Anomalous hairpin formation in an oligodeoxyribonucleotide, Nucleic Acids Res. 13, 8259-8274 (1985).
15. M. Vorličkova, I. Kejnovska, J. Kovanda and J. Kypr, Conformational properties of DNA strands containing guanine-adenine and thymine-adenine repeats, Nucleic Acids Res. 26, 1509-1514 (1998).
16. J. R. Fresco and P. Doty, Molecular properties and configurations of polyriboadenylic acid in solution, J. Am. Chem. Soc. 79, 3928-3929 (1957).
17. J. R. Fresco, The X-ray diffraction patterns of solutions of the randomly coiled and helical forms of polyriboadenylic acid, J. Mol. Biol. 1, 106-110 (1959).
18. A. Rich, D. R. Davies, F. H. C. Crick and J. D. Watson, The molecular structure of polyadenylic acid, J. Mol. Biol. 3, 71-86 (1961).
19. N (U) from the dependence of TN M on oligomer length (see Appendix), Biopolymers 12, 775-789 (1973).
20. J. Brahms, A. M. Michelson and K. E. van Holde, Adenylate oligomers in single-and doublestrand conformation, J. Mol. Biol. 15, 467-488 (1966).
21. H. Robinson and A.H.-J. Wang, 50-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis, Proc. Natl. Acad. Sci. USA 90, 5224-5228 (1993).
22. H. Robinson, J. H. van Boom and A.H.-J. Wang, 50-CGA motif induces other sequences to form homo base-paired parallel-stranded DNA duplex: The structure of (G-A)n derived from four DNA oligomers containing (G-A)3 sequence, J. Am. Chem. Soc. 116, 1565-1566 (1994).
23. W. M. Scovell, Structural and conformational studies of polyriboadenylic acid in neutral and acid solution, Biopolymers 17, 969-984 (1978).
24. D. B. Lerner and D. R. Kearns, Proton and phosphorus NMR investigation of the conformational states of acid polyadenylic double helix, Biopolymers 20, 803-816 (1981).
25. E. M. Evertsz, K. Rippe and T. M. Jovin, Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs, Nucleic Acids Res. 22, 3293-3303 (1994).
26. S. B. Noonberg, J. C. Francois, T. Garestier and C. Hélène, Effect of competing self-structure on triplex formation with purine-rich oligodeoxynucleotides containing GA repeats, Nucleic Acids Res. 23, 1956-1963 (1995).
27. B. Faucon, J.-L. Mergny and C. Hélène, Effect of third strand composition on triple helix formation: purine versus pyrimidine oligodeoxynucleotides, Nucleic Acids Res. 24, 3181-3188 (1996).
28. n DNA sequences: Intramolecular and intermolecular association of the individual strands, J. Mol. Biol. 233, 671-681 (1993).
29. A. I. Murchie and D. M. Lilley, Tetraplex folding of telomere sequences and the inclusion of adenine bases, EMBO J. 13, 993-1001 (1994).
30. 20 DNA sequence, Biochemistry 34, 14408-14415 (1995).
31. S.-H. Chou, L. Zhu, Z. Gao, J.-W. Cheng and B. R. Reid, Hairpin loops consisting of single adenine residues closed by sheared A A and G G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin, J. Mol. Biol. 264, 981-1001 (1996).
32. S.-H. Chou, L. Zhu and B. R. Reid, Sheared purine-purine pairing in biology, J. Mol. Biol. 267, 1055-1067 (1997).
33. M. Katahira, H. Sato, K. Mishima, S. Uesugi and S. Fujii, NMR studies of G A mismatches in oligodeoxyribonucleotide duplexes modelled after ribozymes, Nucleic Acids Res. 21, 5418-5424 (1993).
34. Y. Li, G. Zon and W. D. Wilson, Thermodynamics of DNA duplexes with adjacent G A mismatches, Biochemistry 30, 7566-7572 (1991).
35. J.-W. Cheng, S.-H. Chou and B. R. Reid, Base pairing geometry in GA mismatches depends entirely on the neighboring sequence, J. Mol. Biol. 228, 1037-1041 (1992).
36. S. Ebel, A. N. Lane and T. Brown, Very stable mismatch duplexes: structural and thermodynamic studies on tandem G A mismatches in DNA, Biochemistry 31, 12083-12086 (1992).
37. H. A. Heus, S. S. Wijmenga, H. Hoppe and C. W. Hilbers, The detailed structure of tandem G A mismatched base-pair motifs in RNA duplexes is context dependent, J. Mol. Biol. 271, 147-158 (1997).
38. 2 by twodimensional NMR and the iterative relaxation matrix approach, Biochemistry 36, 4449-4460 (1997).
39. S.-H. Ke and R. M. Wartell, The thermal stability of DNA fragments with tandem mismatches at a d(CXYG).d(CY0X0G) site, Nucleic Acids Res. 24, 707-712 (1996).
40. L. S. Kan, S. Chandrasegaran, S. M. Pulford and P. S. Miller, Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy, Proc. Natl. Acad. Sci. USA 80, 4263-4265 (1983).
41. G. G. Privé, U. Heinemann, S. Chandrasegaran, L. S. Kan, M. L. Kopka and R. E. Dickerson, Helix geometry, hydration, and G.A mismatch in a B-DNA decamer, Science 238, 498-504 (1987).
42. E. P. Nikonowicz and D. G. Gorenstein, Two-dimensional proton and phosphorus-31 NMR spectra and restrained molecular dynamics structure of a mismatched GA decamer oligodeoxyribonucleotide duplex, Biochemistry 29, 8845-8858 (1990).
43. T. Brown, W. N. Hunter, G. Kneale and O. Kennard, Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations, Proc. Natl. Acad. Sci. USA 83, 2402-2406 (1986).
44. G. D. Webster, M. R. Sanderson, J. V. Skelly, S. Neidle, P. F. Swann, B. F. Li and I. J. Tickle, Crystal structure and sequence-dependent conformation of the A G mispaired oligonucleotide d(CGCAAGCTGGCG), Proc. Natl. Acad. Sci. USA 87, 6693-6697 (1990).
45. T. Brown, G. A. Leonard, E. D. Booth and J. Chambers, Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs, J. Mol. Biol. 207, 455-457 (1989).
46. X. Gao and D. J. Patel, G(syn), A(anti) mismatch formation in DNA dodecamers a acidic pH: pH-dependent conformational transition of G A mispairs detected by proton NMR, J. Am. Chem. Soc. 110, 5178-5182 (1988).
47. I. Hirao, Y. Nishimura, T. Naraoka, K. Watanabe, Y. Arata and K. Miura, Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC), Nucleic Acids Res. 17, 2223-2231 (1989).
48. P. Sandusky, E. W. Wooten, A. V. Kurochkin, T. Kavanaugh, W. Mandecki and E. R. Zuiderweg, Occurrence, solution structure and stability of DNA hairpins stabilized by a GA/CG helix unit, Nucleic Acids Res. 23, 4717-4725 (1995).
49. I. Hirao, M. Ishida, K. Watanabe and K. Miura, Unique hairpin structures occurring at the replication origin of phage G4 DNA, Biochim. Biophys. Acta 1087, 199-204 (1990).
50. M. Ortiz-Lombardía, A. Cortés, D. Huertas, R. Eritja and F. Azorín, Tandem 50-GA:GA-30 mismatches account for the high stability of the fold-back structures formed by the centromeric Drosophila dodeca-satellite, J. Mol. Biol. 277, 757-762 (1998).
51. E. Henderson, C. C. Hardin, S. K. Walk, I. Tinoco and E. H. Blackburn, Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs, Cell 51, 899-908 (1987).
52. W. I. Sundquist and A. Klug, Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops, Nature 342, 825-829 (1989).
53. S. Yoshizawa, G. Kawai, K. Watanabe, K. Miura and I. Hirao, GNA trinucleotide loop sequences producing extraordinarily stable DNA minihairpins, Biochemistry 36, 4761-4767 (1997).
54. I. Hirao, G. Kawai, S. Yoshizawa, Y. Nishimura, Y. Ishido, K. Watanabe and K. Miura, Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat, Nucleic Acids Res. 22, 576-582 (1994).
55. n repeats form intramolecular hairpins stabilized by different basepairing interactions, Biochemistry 35, 13125-13135 (1996).
56. J. R. Fresco, L. C. Klotz and E. G. Richards, A new spectroscopic approach to the determination of helical secondary structure in ribonucleic acids, Cold Spring Harbor Symp. Quant. Biol. 28, 83-90 (1963).
57. n DNAs on lowering the pH are three-stranded, Nucleic Acids Res. 6, 3073-3091 (1979).
58. J. S. Lee, D. H. Evans and A. R. Morgan, Polypurine DNAs and RNAs form secondary structures which may be tetra-stranded, Nucleic Acids Res. 8, 4305-4320 (1980).
59. J. S. Lee, The stability of polypurine tetraplexes in the presence of mono-and divalent cations, Nucleic Acids Res. 18, 6057-6060 (1990).
60. I. Mukerji, M. C. Shiber, J. R. Fresco and T. G. Spiro, A UV resonance Raman study of hairpin dimer helices of d(A-G)10 at neutral pH containing intercalated dA residues and alternating dG-tetrads, Nucleic Acids Res. 24, 5013-5020 (1996).
61. L. A. Klobutcher, M. T. Swanton, P. Donini and D. M. Prescott, All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 30 terminus, Proc. Natl. Acad. Sci. USA 78, 3015-3019 (1981).
62. F. W. Smith and J. Feigon, Quadruplex structure of Oxytricha telomeric DNA oligonucleotides, Nature 356, 164-168 (1992).
63. G. R. Sutherland and R. I. Richards, Dynamic mutations: A newly discovered class of genetic mutations provides fresh insight into the curious inheritance patterns of some human diseases, Am. Sci. 82, 157-163 (1994).