Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: Thermodynamic analysis of effects of coulombic interactions and alpha-helix induction

Coulombic interactions and coupled conformational changes make important contributions to stability and specificity of many protein-nucleic acid complexes. As models of these phenomena in simpler systems, we have investigated the binding to mononucleosomal (160 base-pair) calf thymus DNA of a high charge density (compact) 5-residue (+4) oligopeptide (with 4 lysines and 1 tryptophan) and of four lower charge density (extended) 17-residue (+4) oligopeptides (each with 4 lysines, 10-12 alanines, 0-2 glycines, and 1 tryptophan). The fractional helicity (f(h)) of each oligopeptide before and after DNA binding was determined using circular dichroism. At low univalent cation concentration ([M+] = 6.4 mM), binding to DNA increases f(h) significantly for all but one of the extended oligopeptides. Oligopeptide-DNA binding constants (K-obs) and apparent binding site sizes (n) were quantified using the noncooperative McGhee-von Hippel isotherm to fit tryptophan fluorescence quenching data. For each of the oligopeptides studied; n is found to be approximately equal to four, the number of lysine charges. In the range 6.4 mM less than or equal to [M+] less than or equal to 21.5 mM, power dependences of K-obs on [M+] (SKobs = d log K-obs/d log[M+]) for all 17-residue (+4) oligopeptides are similar with an average value of -3.7 +/- 0.4, which is indistinguishable (outside uncertainty) from the value obtained here for the compact (+4) oligopeptide and from values reported elsewhere for another compact tetralysine and for spermine (+4). Our results are consistent with the conclusion that the nonspecific binding to DNA of all these tetravalent ligands is driven primarily by coulombic interactions, At any [M+] investigated, values of K-obs for the four extended (+4) oligopeptides differ by less than an order of magnitude, but all are 1-2 orders of magnitude less than values of K-obs for two compact (+4) oligopeptides and for spermine. The differences in K-obs for oligopeptide-DNA complexes, which all have similar n and similar SKobs, indicate that when an extended oligopeptide binds to DNA it becomes more compact as a result of conformational changes, such as the additional alpha-helix formation detected by circular dichroism.