Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

NMR Study on Binding of Alkali Cations to G-quadruplex formed by d(G4T4G3)

The formation of non-B-form DNA secondary structures, such as formation of quadruplex structures by G-rich repeat sequences, is greatly dependent on DNA-cation interactions. We have studied the folding and solution-state structure of the DNA oligonucleotide d(G4T4G3). This molecule was found to form a quadruplex structure with three guanine quartets, but with a fold that was distinct from that assumed by the closely related molecules d(G4T4G4) and d(G3T4G3).(1-3) From numerous experiments with variations in sample concentration and solution conditions we have determined that d(G4T4G3) can adopt at least two distinct folds. The presence of each fold depends upon several factors, including the species of associated cation, the pathway by which the molecule was folded, and time from sample preparation. The number of cations bound by d(G4T4G3) and their location within its biomolecular structure is fold-dependent and can resemble the coordination of three cations like d(G4T4G4), or two like d(G3T4G3). The number of cations bound by d(G4T4G3) and their location within its biomolecular structure was studied with the use of recently developed technique for the localization of cation binding on nucleic acids using the isotopically 15N labeled ammonium ion as a chemical probe in NMR experiments.(4) Our results suggest that at least some of numerous speculations on the role of DNA quadruplexes in vivo based upon in vitro experiments are only applicable to a very small set of sample conditions, and that the folding of DNA molecules that contain G-quartets may be even more sensitive to solution conditions than previously appreciated.

References and Footnotes
  1. Smith, F. W.; Feigon, J. Nature 1992, 356, 164.
  2. Smith, F. W.; Lau, F. W.; Feigon, J. Proc. Natl. Acad. Sci. USA 1994, 91, 10546.
  3. Strahan, G. D.; Shafer, R. H.; Keniry, M. A. Nucl. Acids Res. 1994, 22, 5447.
  4. Hud, N. V.; Schultze, P.; Sklenar, V.; Feigon, J. J. Mol. Biol. 1999, 285, 233.

Martin Crnugelj (1), Nicholas V. Hud (2) and Janez Plavec (1)

(1) NMR center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia, Phone: +386-1-47-60-353, Fax: +386-1-42-59-244, E-mail: janez.plavec@ki.si (2) School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA, Phone: +1-404-385-1162, Fax: +1-404-894-2295, E-mail: hud@chemistry.gatech.edu