The importance of coulombic end effects: Experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (L8+) binding to single-stranded DNA oligomers

Binding constants K-obs, expressed per site and evaluated in the limit of z ero binding density, are quantified as functions of salt (sodium acetate) c oncentration for the interactions of the oligopeptide ligand KWK6NH2 (desig nated L8+, 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 t he first systematic experimental information about the effect of changing I Z,I on the strength and salt dependence of oligocation-oligonucleotide bind ing interactions. In a comparative study of L8+ 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 pho sphate charges that flank isolated nonspecific L8+ binding sites on DNA. He re we find that both K-obs and the magnitude of its power dependence on sal t activity (/SaKobs/) increase monotonically with increasing /Z(D)/. The de pendences of K-obs and SaKobs on /Z(D)/ are interpreted by introducing a si mple two-state thermodynamic model for Coulombic end effects, which account s for our finding that when L8+ binds to sufficiently long dT-mers, both De lta G(obs)(o) = -RT In K-obs and SaKobs approach the Values characteristic of binding to poly-dT as linear functions of the reciprocal of the number o f 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 rang e of the Coulombic end effect for ss DNA extends over similar to 10 phospha te charges. We conclude that Coulombic interactions cause an oligocation (w ith Z(L) < /Z(D)/) to bind preferentially to interior rather than terminal binding sites on oligoanionic or polyanionic DNA, and we quantify the stron g increase of this preference with decreasing salt concentration. Coulombic end effects must be considered when oligonucleotides are used as models fo r polyanionic DNA in thermodynamic studies of the binding of charged ligand s, including proteins.