Site-resolved stabilization of a DNA triple helix by magnesium ions.
Proton exchange and NMR spectroscopy have been used to define the effects of Mg2+ ions upon the stability of individual base pairs in the intramolecular parallel triple helix formed by the DNA oligonucleotide d(GAAGAGGTTTTTCCTCTTCTTTTTCTTCTCC). The rates of exchange of individual Watson-Crick and Hoogsteen imino protons in the DNA triple helix were measured in the absence and in the presence of Mg2+ ions. The results reveal that Mg2+ lowers the exchange rates of most imino protons in the structure by stabilizing the corresponding base pairs in their native closed conformation. Comparison of the DNA triple helix containing Na+ counterions to the same helix containing Mg2+ counterions shows that these stabilizing effects result, in large part, from Mg2+ ions closely associated with the DNA. Moreover, the effects are site-specific and depend on the number and location of protonated cytosines relative to the observed base. These findings provide new insights into the molecular roles of C+*GC triads in determining the stability of DNA triple-helical structures.
Coman
Daniel
D
Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA.
Russu
Irina M
IM
D020029:Base Pairing; D001483:Base Sequence; D002413:Cations, Divalent / Q000494:pharmacology; D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D008274:Magnesium / Q000494:pharmacology*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011522:Protons
D002413:Cations, Divalent; D011522:Protons; C051802:triplex DNA; D004247:DNA; D008274:Magnesium