Comparison of the solution and crystal conformations of (G + C)-rich fragments of DNA

Biophysical Journal

Volumn 71, Issue 3, 1996, Pages 1530-1538

  Vorlíčková, Michaela ^a   Subirana, Juan A ^b   Chládková, Jana ^a   Tejralová, Iva ^a   Huynh Dinh, Tam ^c   Arnold, Luboš ^d   Kypr, Jaroslav ^a  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

^b UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^c INSTITUT PASTEUR   (France)

^d INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA FRAGMENT; OLIGODEOXYNUCLEOTIDE;

AQUEOUS SOLUTION; ARTICLE; CIRCULAR DICHROISM; CRYSTAL STRUCTURE; DNA CONFORMATION;

EID: 0029774108     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79355-4     Document Type: Article

References (52)

1. Basham, B., G. P. Schroth, and P. S. Ho. 1995. An A-DNA triplet code. thermodynamic rules for predicting A- and B-DNA. Proc. Natl. Acad. Sci. USA. 92:6464-6468.
2. Bayley, P. M., and S. R. Martin. 1992. The α-helical content of calmodulin is increased by solution conditions favouring protein crystallization. Biochim. Biophys. Acta. 1160:16-21.
3. Benevides, J. M., A. H.-J. Wang, A. Rich, Y. Kyogoku, G. A. van der Marel, J. H. van Boom, and G. J. Thomas, Jr. 1986. The Raman spectra of single crystals of r(GCG)d(CGC) and d(CCCCGGGG) as model for A-DNA, their structure transitions in aqueous solution and comparison with double helical poly(dG)·poly(dC). Biochemistry. 25:41-50.
4. Biburger, M., M. Niederweis, and W. Hillen. 1994. Oligo(dC)·oligo(dG) runs exhibit a helical repeat of 11.1 bp in solution and cause slight DNA curvature when properly phased. Nucleic Acids Res. 22:1562-1566.
5. Borden, K. L. B. 1993. The activating transcription factor region within the E2A promoter exist in a novel conformation. Biochemistry. 32: 6506-6514.
6. Borer, P. N. 1975. Optical properties of nucleic acids, absorption, and circular dichroism spectra. In Handbook of Biochemistry and Molecular Biology, Vol. 1. G. D. Fasman, editor. CRC Press, Boca Raton. 589.
7. Bourtayre, P., J. Liguier, L. Pizzorni, and E. Taillandier. 1987. Z-form of poly(dA-dT) in solution studied by CD and CV spectroscopy. J. Biomol. Struct. Dyn. 5:97-104.
8. 2: a combined X-ray and NMR study. Nucleic Acids Res. 18:5521-5528.
9. Davis, P. W., K. Hall, P. Cruz, I. Tinoco, Jr., and T. Neilson. 1986. The tetraribonucleotide r(CGCG) forms a left-handed Z-RNA double helix. Nucleic Acids Res. 14:1279-1291.
10. 2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling. Nucleic Acids Res. 21:569-576.
11. Fairall, L., and J. T. Finch. 1992. Single crystals of long DNA molecules. J. Biomol. Struct. Dyn. 9:633-642.
12. Fairall, L., S. Martin, and D. Rhodes. 1989. The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure. EMBO J. 8:1809-1817.
13. Gray, D. M., and R. L. Ratliff. 1975. Circular dichroism spectra of poly[d(AC):d(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.
14. Gray, D. M., I. Tinoco, Jr., and M. J. Chamberlin. 1972. The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation. Biopolymers. 11:1235-1258.
15. Hall, K., P. Cruz, I. Tinoco, Jr., T. M. Jovin, and J. H. van de Sande. 1984. "Z-RNA" - a left-handed RNA double helix. Nature. 311:584-586.
16. Haran, T. E., and Z. Shakked. 1988. Sequence-dependent effects in ADNA double helices. J. Mol. Struct. (Thenohem.). 179:367-391.
17. Heinemann, U., C. Alings, and H. Lauble. 1990. Structural features of G/C-rich DNA going A or B. In Structure and Methods, Vol. 3: DNA and RNA. R. H. Sarma and M. H. Sarma, editors. Adenine Press, New York. 39-53.
18. Ho, P. S., T. F, Kagawa, K. Tseng, G. P. Schroth, and G. Zhou. 1991. Prediction of a crystallization pathway for Z-DNA hexanucleotides. Science. 254:1003-1006.
19. Huber, P. W., G. C. Blobe, and K. M. Hartmann. 1991. Conformational studies of the nucleic acid binding sites for Xenopus transcription factor IIIA. J. Biol. Chem. 266:3278-3286.
20. Ivanov, V. I., D. Yu. Krylov, and E. E. Minyat. 1985. Three-state diagram for DNA. J. Biomol. Struct. Dyn. 3:43-55.
21. Ivanov, V. I., D. Yu. Krylov, E. E. Minyat, and L. E. Minchenkova. 1983. B-A transition in DNA. J. Biomol. Struct. Dyn. 1:453-460.
22. Ivanov, V. I., L. E. Minchenkova, E. E. Minyat, M. D. Frank-Kamenetskii, and A. Schyolkina. 1974. The B-to-A transition of DNA in solution. J. Mol. Biol. 87:817-833.
23. 3T). Proc. Natl. Acad. Sci. USA. 89:8832-8836.
24. Lu, M., Q. Guo, and N. R. Kallenbach. 1993. Thermodynamics of G-tetraplex formation by telomeric DNAs. Biochemistry. 32:598-601.
25. Malenkov, G., L. Minchenkova, E. Minyat, A. Schyolkina, and V. Ivanov. 1975. The nature of the B-A transition of DNA in solution. FEBS Lett. 51:38-42.
26. Malinina, L., L. Urpi, X. Salas, T. Huynh-Dinh, and J. A. Subirana. 1994. Recombination-like structure of d(CCGCGG). J Mol. Biol. 243: 484-493.
27. Minchenkova, L. E., A. K. Schyolkina, B. K. Chemov, and V. I. Ivanov. 1986. CC/GG contacts facilitate the B-to-A transition of DNA in solution. J. Biomol. Struct. Dyn. 4:463-476.
28. Minyat, E. E., V. I. Ivanov, A. M. Kritzyn, L. E. Minchenkova, and A. K. Schyolkina. 1978. Spermine and spermidine-induced B-to-A transition of DNA in solution. J. Mol. Biol. 128:397-409.
29. Mitsui, Y., R. Langridge, B. E. Shortle, C. R. Cantor, R. C. Grant, M. Kodama, and R. D. Wells. 1970. Physical and enzymatic studies on poly(dI-dC)·poly(dI-dC), an unusual double-helical DNA. Nature. 228: 1166-1169.
30. Ott, G., L. Arnold, J. Smrt, M. Sobkowski, S. Limmer, H. P. Hofmann, and M. Sprinzl. 1993. The chemical synthesis of biochemically active oligoribonucleotides using dimethylaminomethylene protected purine H-phosphonates. Nucleosides Nucleotides. 13:1069-1085.
31. Peticolas, W. L., Y. Wang, and G. A. Thomas. 1988. Some rules for predicting the base-sequence dependence of DNA conformation. Proc. Natl. Acad. Sci. USA. 85:2579-2583.
32. Pohl, F. M., and T. M. Jovin. 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.
33. Riazance, J. H., W. C. Johnson, Jr., L. P. McIntosh, and T. M. Jovin. 1987. Vacuum UV circular dichroism is diagnostic for the left-handed Z-form of poly[d(A-C)·d(G-T)] and other polydeoxynucleotides. Nucleic Acids Res. 15:7627-7636.
34. Rinkel, L. J., M. R. Sanderson, G. A. van der Marel, J. H. van Boom, and C. Altona. 1986. Conformational analysis of the octamer d(GGCCGGCC) in aqueous solution. Eur. J. Biochem. 159:85-93.
35. Sato, M., A. Ono, H. Higuchi, and T. Ueda. 1986. CD spectra and some properties of deoxyoligonucleotide duplexes having a C:G terminus. Nucleic Acids Res. 14:1405-1416.
36. Shakked, Z., D. Rabinovich, W. B. T. Cruse, E. Egert, O. Kennard, G. Sala, S. A. Salisbury, and M. A. Viswamitra. 1981. Crystalline A-DNA: the X-ray analysis of the fragment d(GGTATACC). Proc. R. Soc. Lond. B. 213:479-487.
37. Sprous, D., W. Zacharias, Z. A. Wood, and S. C. Harvey. 1995. Dehydrating agents sharply reduce curvature in DNAs containing A-tracts. Nucleic Acids Res. 23:1816-1821.
38. Sutherland, J. C., and K. P. Griffin. 1983. Vacuum ultraviolet circular dichroism of poly(dI-dC)·poly(dI-dC): no evidence for a left-handed double helix. Biopolymers. 22:1445-1448.
39. Thomas, T. J., and R. P. Messner. 1986. A left-handed (Z) conformation of poly(dA-dC)·poly(dG-dT) induced by polyamines. Nucleic Acids Res. 14:6721-6733.
40. Tomasz, M., J. K. Barton, C. C. Magliozzo, D. Tucker, E. M. Lafer, and B. D. Stollar. 1983. Lack of Z-DNA conformation in mitomycin-modified polynucleotides having inverted circular dichroism. Proc. Natl. Acad. Sci. USA. 80:28474-2878.
41. Trulson, M. O., P. Cruz, J. D. Puglisi, I. Tinoco, Jr., and R. A. Mathies. 1987. Raman spectroscopic study of left-handed Z-RNA. Biochemistry. 26:8624-8630.
42. Uesugi, S., M. Ohkubo, E. Ohtsuka, M. Ikehara, Y. Kobayashi, Y. Kyogoku, H. P. Westerink, G. A. van der Marel, J. H. van Boom, and C. A. G. Haasnoot. 1984. Conformation of ribooligonucleotide duplexes containing an alternating C-G sequence which show an unusual circular dichroism spectrum. J. Biol. Chem. 259:1390-1393.
43. Urpi, L., J. P. Ridoux, J. Liquier, N. Verdaguer, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh-Dinh, J. Igolen, and E. Taillandier. 1989. Conformations in crystals and solutions of d(CACGTG), d(CCGCGG) and d(GGCGCC) studied by vibrational spectroscopy. Nucleic Acids Res. 17: 6669-6680.
44. Verdaguer, N., J. Aymami, D. Fernandez-Forner, I. Fita, M. Coll, T. Huynh-Dinh, J. Igolen, and J. A. Subirana. 1991. Molecular structure of a complete turn of A-DNA. J. Mol. Biol. 221:623-635.
45. Vorlíčková, M. 1995. Conformational transitions of alternating purine-pyrimidine DNAs in perchlorate ethanol solutions. Biophys. J. 69: 2033-2043.
46. 5dU) in solution. Nucleic Acids Res. 20:1109-1112.
47. Vorlíčková, M., J. Kypr, and T. M. Jovin. 1990. CD of the synthetic RNA duplexes poly[r(A-T) and poly[r(A-U)] in salt and ethanolic solutions. Biopolymers. 29:385-392.
48. 5dC) among and within the B-, Z-, A- and X-DNA families of conformations. Nucleic Acids Res. 19:2343-2347.
49. Vorlíčková, M., J. Sági, I. Hejtmánková, and J. Kypr. 1991. Alkyl substituent in place of the thymine methyl group controls the A-X Conformational bimorphism in poly(dA-dT). J. Biomol. Struct. Dyn. 9:571-578.
50. Wang, A. H.-J., G. J. Quigley, F. J. Kolpak, J. L. Crawford, J. H. van Boom, G. van der Marel, and A. Rich. 1979. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 282:680-686.
51. Westhof, E., and M. Sundaralingam. 1984. Proflavine binding to poly(rC-rA) inverts the CD spectrum but not the helix handedness. J. Biomol. Struct. Dyn. 2:159-164.
52. 3), a B-family duplex in solution. Biochemistry. 28:2452-2459.