Conformational properties of Z-forming DNA oligomers bearing terminal unpaired bases

Biophysical Journal

Volumn 71, Issue 6, 1996, Pages 3361-3369

  Marotta, Stephen P ^a   Sheardy, Richard D ^a  

^a SETON HALL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE; DNA; OLIGOMER; SODIUM CHLORIDE;

ARTICLE; CIRCULAR DICHROISM; CONFORMATION; CONTROLLED STUDY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; TEMPERATURE; THERMODYNAMICS; TITRIMETRY;

EID: 0029769802     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79529-2     Document Type: Article

References (20)

1. 5C). Proc. Natl. Acad. Sci. USA. 78:1619-1623.
2. Caruthers, M. H. 1991. Chemical synthesis of DNA and DNA analogues. Acc. Chem. Res. 24:274-284.
3. Chen, F-M. 1988. Effects of A:T base pairs on the B-Z conformational transitions of DNA. Nucleic Acids Res. 16:2269-2281.
4. Doktycz, M. J., A. S. Benight, and R. D. Sheardy. 1990a. Energetics of B-Z junction formation in a sixteen base-pair duplex DNA. J. Mol. Biol. 212:3-6.
5. 4 endloops: evaluation of nearest-neighbor stacking interactions in DNA. Biopolymers. 32: 849-864.
6. 4GTATCC-3′, where X, Y = A, T, G, C. Biopolymers. 30:829-845.
7. Freier, S. M., D. Alkema, A. Sinclair, T. Neilson, and D. H. Turner. 1985. Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCp, and XCCGGYp helixes. Biochemistry. 24:4533-4539.
8. 6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs. Biochemistry. 28:5881-5889.
9. Henderson, J. T., A. S. Benight, and S. Hanlon. 1992. A semi-micromethod for the determination of the extinction coefficients of duplex and single-stranded DNA. Anal. Biochem. 201:17-29.
10. Hirao, I., G. Kawai, S. Yoshizawa, Y. Nishimura, Y. Ishido, K. Watanabe, and K. Miura. 1994. 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.
11. Jovin, T. M., L. P. McIntosh, D. J. Arndt-Jovin, D. A. Zarling, M. Robert-Nicoud, J. H. van de Sande, K. F. Jorgenson, and F. Eckstein. 1983. Left-handed DNA: from synthetic polymers to chromosomes. J. Biomol. Struct. Dyn. 1:21-57.
12. Markey, L. A., and K. J. Breslauer. 1987. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 26:1601-1620.
13. 5C-G) in solution. The B, Z, and hairpin forms. J. Biomol. Struct. Dyn. 6:939-963.
14. Petersheim, M., and D. H. Turner. 1983. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 22:256-263.
15. Senior, M., R. A. Jones, and K. J. Breslauer. 1988. Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry. 28:720-725.
16. Sheardy, R. D. 1988. Preliminary spectroscopic characterization of a synthetic DNA oligomers containing a B-Z junction at high salt. Nucleic Acids Res. 16:1153-1167.
17. Sheardy, R. D. 1991. Monitoring conformational transitions in synthetic DNA oligomers using circular dichroism. Spectroscopy. 6:14-17.
18. Sheardy, R. D., D. Suh, R. Kurzinsky, M. J. Doktycz, A. S. Benight, and J. B. Chairs. 1993. Sequence dependence of the free energy of B-Z junction formation in deoxyoligonucleotides. J. Mol. Biol. 231:475-488.
19. Sheardy, R. D., and S. A. Winkle. 1989. Temperature dependent CD and NMR studies on a synthetic DNA oligomer containing a B-Z junction at high salt. Biochemistry. 28:720-725.
20. Wang, Y., G. A. Thomas, and W. L. Peticolas. 1987. Sequence dependence of the B to Z transition in crystal and aqueous NaCl solutions for deoxyoligonucleotides containing all four canonical DNA bases. Biochemistry. 26:5178-5186.