title: Hydration changes accompanying helix-to-coil DNA transitions.
abstract: We applied ultrasonic velocimetric and high-precision densimetric measurements to characterizing the helix-to-coil transition of the GGCATTACGG/CCGTAATGCC decameric DNA duplex. The transition was induced either by temperature or by mixing the two complementary single strands at isothermal conditions. The duplex dissociation causes increases in volume and expansibility while resulting in a decrease in compressibility. Our volumetric data in conjunction with computer-generated structural information are consistent with the picture in which the duplex dissociation is accompanied by an uptake of ∼180 water molecules from the bulk phase into the hydration shell of the DNA. Analysis of our compressibility and expansibility data reveals that the single-stranded conformation is likely to exist as a heterogeneous mixture of nearly isoenergetic subspecies differing in volume and enthalpy. We use our estimate of the change in hydration to evaluate the hydration and configurational contributions to the helix-to-coil transition entropy. The duplex dissociation is accompanied by an increase in configurational entropy, ΔSconf, of ∼23 cal mol(-1) K(-1) per nucleotide, which signifies liberation of manifold frozen degrees of freedom involved in maintaining the conformational stability of the duplex and the related stiffening of the heterocyclic bases and the sugar-phosphate backbone. To the best of our knowledge, this is the first experimental estimate of the change in configurational entropy associated with the helix-to-coil transition of a DNA.
authors.affiliation: Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto , 144 College Street, Toronto, Ontario M5S 3M2, Canada.
authors.forename: Ikbae
authors.initials: I
authors.lastname: Son
authors.forename: Yuen Lai
authors.initials: YL
authors.lastname: Shek
authors.forename: David N
authors.initials: DN
authors.lastname: Dubins
authors.forename: Tigran V
authors.initials: TV
authors.lastname: Chalikian
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D019277:Entropy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D004247:DNA