NMR studies of DNA three-way junctions containing two unpaired thymidine bases: The influence of the sequence at the junction on the stability of the stacking conformers

Journal of Molecular Biology

Volumn 255, Issue 5, 1996, Pages 702-713

  Overmars, Franc J J ^a   Pikkemaat, Jeroen A ^a   Van Den Elst, Hans ^a   Van Boom, Jacques H ^a   Altona, Cornelis ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

1H NMR spectroscopy; Four way junction; Hairpin loop; Oligonucleotide; Three way junction

Indexed keywords

DNA; OLIGOMER; THYMIDINE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA CONFORMATION; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; DNA SYNTHESIS; NUCLEAR MAGNETIC RESONANCE; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE;

EID: 0029962991     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0057     Document Type: Article

References (43)

1. Altona, C. (1990). NMR data on oligonucleotides. In Landolt-Börnstein New Series VII/1c (Saenger, W., ed.), pp. 88-190, Springer-Verlag, Berlin.
2. Altona, C. & Pikkemaat, J. A. (1995). Construction of a DNA four-way junction: design and NMR spectroscopy. In Modelling of Biomolecular Structures and Mechanisms (Pullman et al., eds), pp. 289-304, Kluwer Acad. Publ., Dordrecht, The Netherlands.
3. Bax, A. & Davis, D. G. (1985). MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65, 355-360.
4. Broker, T. R. & Doermann, A. H. (1975). Molecular and genetic recombination of bacteriophage T4. Annu. Rev. Genet. 9, 213-244.
5. Broker, T. R. & Lehman, I. R. (1971). Branched DNA molecules: intermediates in T4 recombination. J. Mol. Biol. 60, 131-149.
6. 1H NMR studies of immobile Holliday junctions: nonlabile proton assignments and identification of crossover isomers. Biochemistry, 33, 11453-11459.
7. 1H NMR studies of synthetic immobile Holliday junctions. Biochemistry, 30, 766-771.
8. Clegg, R. M., Murchie, A. I. H. & Lilley D. M. J. (1994). The solution structure of the four-way DNA junction at low salt conditions: a fluorescence resonance energy transfer analysis. Biophys. J. 66, 99-109.
9. Duckett, D. R. & Lilley D. M. J. (1990). The three-way DNA junction is a Y-shaped molecule in which there is no helix-helix stacking. EMBO J. 9, 1659-1664.
10. Duckett, D. R., Murchie, A. I. H., Diekmann, S., von Kitzing, E., Kemper, B. & Lilley, D. M. J. (1988). The structure of the Holliday junction, and its resolution. Cell, 55, 79-89.
11. Duckett, D. R., Murchie, A. I. H. & Lilley, D. M. J. (1990). The role of metal ions in the conformation of the four-way junction. EMBO J. 9, 583-590.
12. Forster, A. C. & Symons, R. H. (1987). Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell, 49, 211-220.
13. 31P NMR of DNA. Methods Enzymol. 211, 254-286.
14. Guo, Q., Lu, M. & Kallenbach, N. R. (1991). Conformational preference and ligand binding properties of DNA junctions are determined by sequence at the branch. Biopolymers, 31, 359-372.
15. Guthrie, C. & Patterson, B. (1988). Spliceosomal snRNAs. Annu. Rev. Genet. 22, 387-419.
16. Haselhoff, J. & Gerlach, W. L. (1988). Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature, 334, 82-84.
17. Hoess, R., Wierzbicki, A. & Abremski, K. (1987). Isolation and characterization of intermediates in site-specific recombination. Proc. Natl Acad. Sci. USA, 84, 6840-6844.
18. Holliday R. (1964). A mechanism for gene conversion in fungi. Genet. Res. 5, 282-304.
19. Hore, P. J. (1983). Solvent suppression in Fourier transform nuclear magnetic resonance. J.Magn. Reson. 55, 283-300.
20. Ippel, J. H., Lanzotti, V., Galeone, A., Mayol, L., van den Boogaart, J. E., Pikkemaat, J. A. & Altona, C. (1992). An NMR study of the conformation and thermodynamics of the circular dumbbell d. J. Biomol. Struct. Dynam. 9, 821-836.
21. Ippel, J. H., Lanzotti, V., Galeone, A., Mayol, L., van den Boogaart, J. E., Pikkemaat, J. A., Altona, C. (1995). Slow conformational exchange in DNA minihairpin loops, a conformational study of the circular dumbbell d. Biopolymers, 31, 681-693.
22. Jensch, F. & Kemper, B. (1986). Endonuclease VII resolves Y-junctions in branched DNA in vitro. EMBO J. 5, 181-189.
23. Leontis, N. B., Kwok, W. & Newman, J. S. (1991). Stability and structure of three-way DNA junctions containing unpaired nucleotides. Nucleic Acids Res. 19, 759-766.
24. Leontis, N. B., Hills, M. T., Piotto, M., Malhotra, A., Nussbaum, J. & Gorenstein, D. G. (1993). A model for the solution structure of a branched, three-stranded DNA complex. J. Biomol. Struct. Dynam. 11, 215-223.
25. Leontis, N. B., Hills, M. T., Piotto, M., Ouporov, I. V., Malhotra, A. & Gorenstein, D. G. (1995). Helical stacking in DNA three-way junctions containing two unpaired pyrimidines: proton NMR studies. Biophys. J. 68, 251-265.
26. 31P-NMR chemical shifts and infrared spectra of phosphate diesters. Biopolymers, 23, 2157-2172.
27. Lilley, D. M. J. & Clegg, R. M. (1993a). The structure of the four-way junction in DNA. Annu. Rev. Biophys. Biomol. Struct. 22, 299-328.
28. Lilley, D. M. J. & Clegg, R. M. (1993b). The structure of branched DNA species. Quart. Rev. Biophys. 26, 131-175.
29. Lu, M., Guo, Q. & Kallenbach, N. R. (1991). Effect of sequence on the structure of three-arm DNA junctions. Biochemistry, 30, 5815-5820.
30. 1H spin-spin coupling constants in proteins. Biochem. Biophys. Res. Commun. 113, 967-974.
31. Minagawa, T., Murakami, A., Ryo, Y. & Yamagishi, H. (1983). Structural features of very fast sedimenting DNA formed by gene 49 defective T4. Virology, 126, 183-189.
32. Murchie, A. I. H., Clegg, R. M., von Kitzing, E., Duckett, D. R., Diekmann, S., & Lilley D. M. L. (1989). Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature, 341, 763-766.
33. Noller, H. F. (1991). Ribosomal RNA and translation. Annu. Rev. Biochem. 60, 191-227.
34. Orr-Weaver, T. L., Szostak, J. W. & Rothstein, R. J. (1981). Yeast transformation: a model system for the study of recombination. Proc. Natl Acad. Sci. USA, 78, 6354-6358.
35. Ouporov, I. V. & Leontis, N. B. (1995). Refinement of the solution structure of a branched DNA three-way junction. Biophys. J. 68, 266-274.
36. Pieters, J. M. L., de Vroom, E., van der Marel, G. A., van Boom, J. H., Koning, T. M. G., Kaptein, R. & Altona, C. (1990). Hairpin structures in DNA containing arabinofuranosylcytosine. A combination of nuclear magnetic resonance and molecular dynamics. Biochemistry, 29, 788-799.
37. Pikkemaat, J. A., van den Elst, H., van Boom, J. H. & Altona, C. (1994). NMR studies and conformational analysis of a DNA four-way junction formed in a linear synthetic oligonucleotide. Biochemistry, 33, 14896-14907.
38. Rosen, M. A. & Patel, D. J. (1993a). Conformational differences between bulged pyrimidines (C-C) and purines (A-A, I-I) at the branch point of three-stranded DNA junctions. Biochemistry, 32, 6563-6575.
39. Rosen, M. A. & Patel, D. J. (1993b). Structural features of a three-stranded DNA junction containing a C-C junctional bulge. Biochemistry, 32, 6576-6587.
40. Smith, F. W. & Feigon, J. (1993). Strand orientation in the DNA quadruplex formed from the oxytricha telomere repeat oligonucleotide d(G4T4G4) in solution. Biochemistry, 32, 8682-8692.
41. von Kitzing, E., Lilley D. M. J. & Diekmann, S. (1990). The stereochemistry of a four-way DNA junction: a theoretical study Nucl. Acids Res. 18, 2671-2683.
42. Welch, J. B., Duckett, D. R. & Lilley, D. M. J. (1993). Structures of bulged three-way DNA junctions. Nucl. Acids Res. 21, 4548-4555.
43. Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids, John Wiley & Sons, New York.