title: Entropy of water in the hydration layer of major and minor grooves of DNA.
abstract: Transport properties (translational and rotational) of water in the two grooves of the B-DNA duplex are known to be different from those in the bulk. Here, we use a recently developed theoretical scheme to compute the entropies of water molecules in both of the grooves of DNA and compare them with that in the bulk. The scheme requires as input both translational and rotational velocity autocorrelation function (C(V)(t) and C(omega)(t), respectively) data. These velocity autocorrelation functions were computed from an atomistic MD simulation of a B-DNA duplex (36 base pairs long) in explicit water (TIP3P). The average values of the entropy of water at 300 K in both of the grooves of DNA (the TS value in the major groove is 6.71 kcal/mol and that in the minor groove is 6.41 kcal/mol) are found to be significantly lower than that in bulk water (the TS value is 7.27 kcal/mol). Thus, the entropic contribution to the free energy change (TDeltaS) of transferring a minor groove water molecule to the bulk is 0.86 kcal/mol and of transferring a major groove water to the bulk is 0.56 kcal/mol at 300 K, which is to be compared with 1.44 kcal/mol for melting of ice at 273 K. We also calculate the energy of interaction of each water molecule with the rest of the atoms in the system and hence calculate the chemical potential (Helmholtz free energy per water molecule, A = E - TS) in the different domains. The identical free energy value of water molecules in the different domains proves the robustness of the scheme. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or microviscosity) of water molecules in a given domain.
authors.affiliation: Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
authors.forename: Biman
authors.initials: B
authors.lastname: Jana
authors.forename: Subrata
authors.initials: S
authors.lastname: Pal
authors.forename: Prabal K
authors.initials: PK
authors.lastname: Maiti
authors.forename: Shiang-Tai
authors.initials: ST
authors.lastname: Lin
authors.forename: James T
authors.initials: JT
authors.lastname: Hynes
authors.forename: Biman
authors.initials: B
authors.lastname: Bagchi
mesh_terms: D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods; D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D019277:Entropy; D006860:Hydrogen Bonding; D007053:Ice; D008956:Models, Chemical; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D007053:Ice; D014867:Water; D004247:DNA