title: Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA.
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.
authors.affiliation: International Centre for Genetic Engineering and Biotechnology, Padriciano, Italy.
authors.forename: I
authors.initials: I
authors.lastname: Brukner
authors.forename: S
authors.initials: S
authors.lastname: Susic
authors.forename: M
authors.initials: M
authors.lastname: Dlakic
authors.forename: A
authors.initials: A
authors.lastname: Savic
authors.forename: S
authors.initials: S
authors.lastname: Pongor
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002118:Calcium / Q000494:pharmacology; D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D008274:Magnesium / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013329:Structure-Activity Relationship; D014961:X-Ray Diffraction; D015032:Zinc / Q000494:pharmacology
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA; D008274:Magnesium; D015032:Zinc; D002118:Calcium