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Nucleic Acids Research 2004 32(11):3271-3281; doi:10.1093/nar/gkh646
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Published online 17 June 2004

Nucleic Acids Research, Vol. 32 No. 11 © Oxford University Press 2004; all rights reserved

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

Jeff D. Ballin1, Irina A. Shkel1 and M. Thomas Record, Jr1,2,*

1 Department of Chemistry and 2 Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA

* To whom correspondence should be addressed. Tel: +1 608 262 5332; Fax: +1 608 262 3453; Email: record{at}biochem.wisc.edu

Received April 2, 2004; Revised and Accepted May 19, 2004

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 [, 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 {equiv} –{partial}ln Kobs/{partial}ln 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.


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