The detection of B-form/A-form junction in a deoxyribonucleotide duplex

Biophysical Journal

Volumn 71, Issue 6, 1996, Pages 3344-3349

  Ivanov, Valery I ^a   Minchenkova, Lucy E ^a   Burckhardt, Günther ^b   Birch Hirschfeld, Eckhard ^b   Fritzsche, Hartmut ^b   Zimmer, Christoph ^b  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CONGOCIDINE; DEOXYRIBONUCLEOTIDE; DISTAMYCIN A; DNA A; DNA B; DOUBLE STRANDED DNA; TRIFLUOROETHANOL; WATER;

ARTICLE; CIRCULAR DICHROISM; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DRUG DNA BINDING; LIGAND BINDING; NUCLEOTIDE SEQUENCE;

EID: 0029778540     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79527-9     Document Type: Article

References (31)

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. Becker, M. M., and Z. Wang. 1989. B-A transcriptions within a 5s ribosomal RNA gene are highly sequence-specific. J. Biol. Chem. 264: 4263-4267.
3. Brahms, J., and M. F. H. M. Mommaerts. 1964. A study of conformation of nucleic acids in solution by means of circular dichroism. J. Mol. Biol. 58:73-88.
4. 1H NMR study of binding mode and kinetics. J. Med. Chem. 27:450-465.
5. Franklin, R. E., and R. G. Gosling. 1953. The structure of sodium thymonucleate fibers. I. The influence of water content. Acta Crystallogr. 6:673-677.
6. Fritzsche, H. 1994. Infrared linear dichroism studies of DNA-drug complexes: quantitative determination of the drug-induced restriction of the B-A transition. Nucleic Acids Res. 22:787-791.
7. Fritzsche, H., A. Rupprecht, and M. Richter. 1984. Infrared linear dichroism of oriented DNA-ligand complexes prepared with the wet-spinning method. Nucleic Acids Res. 12:9165-9177.
8. Hunter, C. A. 1993. Sequence-dependent DNA structure. The role of base stacking interactions. J. Mol. Biol. 230:1025-1054.
9. Ivanov, V. I., and D. Y. Krylov. 1992. A-DNA in solution as studied by diverse approaches. Methods Enzymol. 211:111-127.
10. Ivanov, V. I., D. Y. Krylov, and E. E. Minyat. 1985. Three-state diagram for DNA. J. Biomol. Struct. Dyn. 3:43-55.
11. Ivanov, V. I., and L. E. Minchenkova. 1995. The A-Form of DNA: in search of biological role (a review). Mol. Biol. 1995:780-788.
12. Ivanov, V. I., L. E. Minchenkova, E. E. Minyat, M. D. Frank-Kamenetskii, and A. K. Schyolkina. 1974. The B to A transition of DNA in solution. J. Mol. Biol. 87:817-833.
13. Ivanov, V. I., L. E. Minchenkova, E. E. Minyat, and A. K. Schyolkina. 1982. Cooperative transitions in DNA with no separation of strands. Cold Spring Harb. Symp. Quant. Biol. 47:243-250.
14. Ivanov, V. I., L. E. Minchenkova, A. K. Schyolkina, and A. I. Poletaev. 1973. Different conformation of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers. 12:89-110.
15. Ivanov, V. I., V. B. Zhurkin, S. K. Zavriev, Y. P. Lysov, L. E. Minchenkova, E. E. Minyat, M. D. Frank-Kamenetskii, and A. K. Schyolkina. 1979. Conformational possibilities of double-helical nucleic acids: theory and experiment. Int. J. Quantum Chem. 16:189-201.
16. Jacobo-Molina, A., J. Ding, R. G. Nanni, A. D. Clark, X. L. Tantillo, R. L. Williams, G. Kramer, A. L. Ferris, P. Clark, A. Hizi, S. H. Hughes, and E. Arnold. 1993. Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution. Proc. Natl. Acad. Sci USA. 90:6320-6324.
17. Krylov, D. Y., V. L. Makarov, and V. I. Ivanov. 1989. The B-A transition in superhelical DNA. Nucleic Acids Res. 18:759-761.
18. Lazurkin, Yu. S., M. D. Frank-Kamenetskii, and E. N. Trifonov. 1970. Melting of DNA: its study and application as a research method. Biopolymers. 9:1253-1306.
19. Luck, G., C. Zimmer, K. E. Reinert, and F. Arcamone. 1977. Specific interactions of distamycin A and its analogs with (A·T) rich and (G·C) rich duplex regions of DNA and deoxypolynucleotides. Nucleic Acids Res. 4:2655-2670.
20. Malenkov, G., L. Minchenkova, E. Minyat, A. Schyolkina, and V. I. Ivanov. 1975. The nature of the B-A transition of DNA in solution. FEBS Lett. 51:38-42.
21. Minchenkova, L. E., A. K. Schyolkina, B. K. Chernov, 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.
22. Minchenkova, L., and C. Zimmer. 1980. Reversion of the B to A transition of DNA induced by specific interaction with the oligopeptide distamycin A. Biopolymers. 19:823-831.
23. Minyat, E. E., V. I. Ivanov, A. M. Kritzyn, L. E. Minchenkova, and A. K. Shyolkina. 1978. Spermine and spermine-induced B to A transition of DNA in solution. J. Mol. Biol. 128:397-409.
24. Pohle, W., V. Zhurkin, and H. Fritzsche. 1984. The DNA phosphate orientation. Infrared data and energetically favorable structures. Biopolymers. 23:2603-2622.
25. Selsing, E., R. D. Wells, C. J. Alden, and S. Arnott. 1979. Bent DNA: visualization of a base-paired and stacked A-B conformational junction. J. Biol. Chem. 254:5417-5422.
26. Sheardy, M. J., D. Suh, R. Kurzinsky, M. J. Doktycz, A. S. Benight, and J. B. Chaires. 1993. Sequence dependence of the free energy of B-Z junction formation in deoxyoligonucleotides. J. Mol. Biol. 231:475-488.
27. Zavriev, S. K., L. E. Minchenkova, M. D. Frank-Kamenetskii, and V. I. Ivanov. 1978. On the flexibility of the boundaries between the A-form and A-form sections in DNA molecule. Nucleic Acids Res. 5:2657-2663.
28. Zhurkin, V. B., N. B. Ulyanov, and V. I. Ivanov. 1988. Mechanism of DNA bending in the free state, and in the nucleosome. In Structure and Expression, W. K. Olson, M. H. Sarma, and R. H. Sarma, editors. Adenine Press, Schenectady, NY. 160-190.
29. Zimmer, C. 1975. Effects of the antibiotics netropsin and distamycin A on the structure and function of nucleic acids. Prog. Nucleic Acids Res. Mol. Biol. 15:285-318.
30. Zimmer, C., G. Luck, E. Birch-Hirschfeld, R. Weiss, F. Arcamone, and W. Guschlbauer. 1983. Chain-length dependent association of distamycin-type oligopeptides with A·T and G·C pairs in polynucleotide duplexes. Biochim. Biophys. Acta. 741:15-22.
31. Zimmer, C., and U. Wähnert. 1986. Nonintercalating DNA binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. Prog. Biophys. Mol. Biol. 47:31-112.