Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA

J Mol Biol. 1994 Feb 11;236(1):26-32. doi: 10.1006/jmbi.1994.1115.

Abstract

The bending propensity of non-A/T DNA sequence elements is well known, but helical phasing/gel mobility experiments fail to reveal an intensive macroscopic curvature if A/T tracts are not present in the sequence. Recent X-ray data prove on the other hand that a GGCC element is intrinsically curved toward the major groove, which seemingly contradicts the fact that macroscopic curvature at GGGCCC elements is hardly detectable with a conventional gel mobility assay. Here we show that GGGCCC containing DNA, with no A/T tracts in the sequence context, has a detectable, strong gel mobility anomaly only in the presence of divalent ions (10 mM Mg2+ or Ca2+, 1 mM Zn2+). Metal ions increase the gel mobility anomaly in A/T tracts as well, but the effect is substantially stronger for GGGCCC than for the rigid A/T tracts. Our data suggest that metal ions change the sequence-dependent dynamic features of DNA; on the other hand, there is no evidence of twist-mediated change of the planarity of curvature in the presence of metal ions. The results show that near-physiological concentrations of divalent cations (10 mM MgCl2) have a strong and differential effect on various sequence elements, so that the current picture of sequence-dependent DNA curvature is changed not only in a quantitative, but also in a qualitative sense.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Base Sequence
  • Calcium / pharmacology
  • DNA / chemistry*
  • DNA / drug effects
  • Magnesium* / pharmacology
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides / chemistry*
  • Structure-Activity Relationship
  • X-Ray Diffraction
  • Zinc / pharmacology

Substances

  • Oligodeoxyribonucleotides
  • DNA
  • Magnesium
  • Zinc
  • Calcium