A high-resolution structure of a DNA-chromomycin-co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance

Structure

Volumn 8, Issue 4, 2000, Pages 441-452

  Gochin, Miriam ^a,b  

^a UNIVERSITY OF THE PACIFIC   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA drug complex; Minor groove binding; Molecular dynamics simulations; Nuclear magnetic resonance; Pseudocontact shift

Indexed keywords

CHROMOMYCIN; COBALT; DNA;

ARTICLE; BASE PAIRING; CARBON NUCLEAR MAGNETIC RESONANCE; COMPLEX FORMATION; DNA DRUG COMPLEX; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE;

EID: 0034656349     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)00124-6     Document Type: Article

References (17)

1. Gao X.L., Patel D.J. Solution structure of the chromomycin-DNA complex. Biochemistry. 28:1989;751-762.
2. Gao X.L., Patel D.J. Chromomycin dimer-DNA oligomer complexes: sequence selectivity and divalent cation specificity. Biochemistry. 29:1990;10940-10956.
3. Gao X.L., Mirau P., Patel D.J. Structure refinement of the chromomycin dimer-DNA oligomer complex in solution. J. Mol. Biol. 223:1992;259-279.
4. Banville D.L., Keniry M.A., Kam M., Shafer R.H. NMR studies of the interaction of chromomycin A3 with small DNA duplexes. Binding to GC-containing sequences. Biochemistry. 29:1990;6521-6534.
5. Itzhaki L., Weinberger S., Livnah N., Berman E. A unique binding cavity for divalent cations in the DNA-metal-chromomycin A3 complex. Biopolymers. 29:1990;481-489.
6. Leroy J.L., Gao X.L., Gueron M., Patel D.J. Proton exchange and internal motions in two chromomycin dimer-DNA oligomer complexes. Biochemistry. 30:1991;5653-5661.
7. Tu K., Gochin M. Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally-determined constraints. J. Am. Chem. Soc. 121:1999;9276-9285.
8. van Wijk J., Huckriede B.D., Ippel J.H., Altona C. Furanose sugar conformations in DNA from NMR coupling constants. Methods Enzymol. 211:1992;286-306.
9. 31P NMR spectra, and determination of electronic, spectroscopic and molecular properties. J. Biomol. NMR. 12:1998;243-257.
10. Schmitz U., Kumar A., James T.L. Dynamic interpretation of NMR data: Molecular Dynamics with weighted time-averaged restraints and 'ensemble' R-factor. J. Am. Chem. Soc. 114:1992;10556-10564.
11. 12 through the use of new two-dimensional NMR experiments. J. Am. Chem. Soc. 108:1986;4285-4294.
12. Kupke E., Freeman R. An adaptable NMR broadband decoupling scheme. Chem. Phys. Lett. 250:1996;523-527.
13. Delaglio F., Grzesiek S, Vuister G.W., Zhu G., Pfeifer J., Bax A NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6:1995;277-293.
14. Goddard T., Kneller D. SPARKY 3.0. 1997;University of California, San Francisco.
15. Gochin M., Roder H. Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c. Protein Sci. 4:1995;296-305.
16. Brünger A.T. X-PLOR 3.1. 1992;Yale University, New Haven, CT.
17. Lavery R., Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6:1988;63-91.