title: Monovalent cation size and DNA conformational stability.
abstract: The effect of monovalent cations on the thermal stability of a small model DNA hairpin has been measured by capillary electrophoresis, using an oligomer with 16 thymine residues as an unstructured control. The melting temperature of the model hairpin increases approximately linearly with the logarithm of increasing cation concentration in solutions containing Na(+), K(+), Li(+), NH(4)(+), Tris(+), tetramethylammonium (TMA(+)), or tetraethylammonium (TEA(+)) ions, is approximately independent of cation concentration in solutions containing tetrapropylammonium (TPA(+)) ions, and decreases with the logarithm of increasing cation concentration in solutions containing tetrabutylammonium (TBA(+)) ions. At constant cation concentration, the melting temperature of the DNA model hairpin decreases in the order Li(+) ∼ Na(+) ∼ K(+) > NH(4)(+) > TMA(+) > Tris(+) > TEA(+) > TPA(+) > TBA(+). Isothermal studies indicate that the decrease in the hairpin melting temperature with increasing cation hydrophobicity is not due to saturable, site-specific binding of the cation to the random coil conformation, but to the concomitant increase in cation size with increasing hydrophobicity. Larger cations are less effective at shielding the charged phosphate residues in B-form DNA because they cannot approach the DNA backbone as closely as smaller cations. By contrast, larger cations are relatively more effective at shielding the phosphate charges in the random coil conformation, where the phosphate-phosphate distance more closely matches cation size. Hydrophobic interactions between alkylammonium ions interacting electrostatically with the phosphate residues in the coil may amplify the effect of cation size on DNA thermal stability.
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States.
authors.forename: Earle
authors.initials: E
authors.lastname: Stellwagen
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Muse
authors.forename: Nancy C
authors.initials: NC
authors.lastname: Stellwagen
mesh_terms: D001483:Base Sequence; D002414:Cations, Monovalent / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004305:Dose-Response Relationship, Drug; D057927:Hydrophobic and Hydrophilic Interactions; D055029:Inverted Repeat Sequences; D008672:Metals, Alkali / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D010710:Phosphates / Q000737:chemistry; D000644:Quaternary Ammonium Compounds / Q000737:chemistry / Q000494:pharmacology; D012996:Solutions; D055672:Static Electricity; D044366:Transition Temperature / Q000187:drug effects
chemical_list: D002414:Cations, Monovalent; D008672:Metals, Alkali; D010710:Phosphates; D000644:Quaternary Ammonium Compounds; D012996:Solutions; D004247:DNA