Incorporation of cationic chains in the Dickerson-Drew dodecamer: Correlation of energetics, structure, and ion and water binding

Ronald Shikiya, Jian Sen Li, Barry Gold, Luis A. Marky

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

We have investigated the unfolding thermodynamics for incorporating cationic side chains in the Dickerson-Drew dodecamer duplex. Incorporation of two 3-aminopropyl-2′-deoxyuridine residues (one on each self-complementary strand) lowers the stability of the duplex. This reduction is driven by unfavorable heat contributions due to the removal of electrostricted water and higher exposure of polar and nonpolar atomic groups that immobilize structural water. These cationic chains effectively remove counterions from the major groove, neutralizing some negatively charged phosphates. The overall results are consistent with the NMR solution of the modified duplex that showed a small bend at each modified site.

Original languageEnglish (US)
Pages (from-to)12582-12588
Number of pages7
JournalBiochemistry
Volume44
Issue number37
DOIs
StatePublished - Sep 20 2005

ASJC Scopus subject areas

  • Biochemistry

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