title: Incorporation of cationic chains in the Dickerson-Drew dodecamer: correlation of energetics, structure, and ion and water binding.
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.
authors.affiliation: Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA.
authors.forename: Ronald
authors.initials: R
authors.lastname: Shikiya
authors.forename: Jian-Sen
authors.initials: JS
authors.lastname: Li
authors.forename: Barry
authors.initials: B
authors.lastname: Gold
authors.forename: Luis A
authors.initials: LA
authors.lastname: Marky
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D003857:Deoxyuridine / Q000031:analogs & derivatives; D007477:Ions; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water
chemical_list: D007477:Ions; D009838:Oligodeoxyribonucleotides; D014867:Water; C053601:5-(3-aminopropyl)-2'-deoxyuridine; D003857:Deoxyuridine