The Importance of Coulombic End Effects: Experimental Characterization of the Effects of Oligonucleotide Flanking Charges on the Strength and Salt Dependence of Oligocation (L 8+) Binding to Single-Stranded DNA Oligomers

Abstract

Binding constants K obs, expressed per site and evaluated in the limit of zero binding density, are quantified as functions of salt (sodium acetate) concentration for the interactions of the oligopeptide ligand KWK 6NH 2 (designated L 8+, with Z L = 8 charges) with three single-stranded DNA oligomers (ss dT-mers, with | Z D| = 15, 39, and 69 charges). These results provide the first systematic experimental information about the effect of changing | Z D| on the strength and salt dependence of oligocation-oligonucleotide binding interactions. In a comparative study of L 8+ binding to poly dT and to a short dT oligomer (| Z D| = 10), Zhang et al. (1996. Proc. Natl. Acad. Sci. USA. 93:2511–2516) demonstrated the profound thermodynamic effects of phosphate charges that flank isolated nonspecific L 8+ binding sites on DNA. Here we find that both K obs and the magnitude of its power dependence on salt activity (| S a K obs|) increase monotonically with increasing | Z D|. The dependences of K obs and S a K obs on | Z D| are interpreted by introducing a simple two-state thermodynamic model for Coulombic end effects, which accounts for our finding that when L 8+ binds to sufficiently long dT-mers, both Δ G obs o = −RT ln K obs and S a K obs approach the values characteristic of binding to poly-dT as linear functions of the reciprocal of the number of potential oligocation binding sites on the DNA lattice. Analysis of our L 8+-dT-mer binding data in terms of this model indicates that the axial range of the Coulombic end effect for ss DNA extends over ∼10 phosphate charges. We conclude that Coulombic interactions cause an oligocation (with Z L < | Z D|) to bind preferentially to interior rather than terminal binding sites on oligoanionic or polyanionic DNA, and we quantify the strong increase of this preference with decreasing salt concentration. Coulombic end effects must be considered when oligonucleotides are used as models for polyanionic DNA in thermodynamic studies of the binding of charged ligands, including proteins.