Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: Demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt

Abstract

We quantify Coulombic end effects (CEE) on oligocation-nucleic acid interactions at salt concentrations ([salt]) in the physiological range. Binding constants (Kobs; per site, at zero binding density) for the +8-charged C-amidated oligopeptide KWK6 and short single-stranded DNA oligonucleotides [dT(pdT)ZD, where 6 ≤ ZD ≤ 22 is the number of DNA phosphates] were determined as a function of [salt] by fluorescence quenching. For the different DNA oligomers, Kobs values are similar at high [salt], but diverge as [salt] decreases because -SaKobs ≡ -∂In Kobs/∂In a± increases strongly with ZD . For binding of KWK6 near 0.1 M salt, -SaKobs is 5.5 ± 0.2 for dT(pdT 22, 4.0 ± 0.2 for dT(pdT)10 and 2.9 ± 0.2 for dT(pdT)6, as compared with 6.5 ± 0.3 for poly(dT). Similarly, at 0.1 M salt, Kobs per site for poly(dT exceeds Kobs for dT(pdT)22 by 7-fold, for dT(pdT 10 by 50-fold and for dT(pdT)6 by 700-fold. We interpret the reductions in Kobs and SaKobs with decreasing ZD as a significant CEE that causes binding to the terminal regions of a nucleic acid to be weaker and less salt dependent than interior binding. We analyze long oligonucleotide-KWK6 binding data in terms of a trapezoidal model for the local (axial) salt cation concentration on single-stranded DNA to estimate the size of the CEE to be at least seven phosphates on each end at 0.1 M salt. © Oxford University Press 2004; all rights reserved.