Molecular Rigidity, Excess Entropy, and Enthalpy-Entropy Compensation in DNA Melting

Published

September 24, 2017

Author(s)

Jack F. Douglas, Fernando Vargas-Lara, Francis W. Starr

Abstract

Enthalpy-entropy compensation (EEC) is observed in diverse molecular binding processes of vital importance to living systems and manufacturing applications, but this widely occurring phenomenon is not well understood from a molecular physics standpoint. To address this fundamental problem, we focus on the melting of double stranded DNA (dsDNA) since measurements exhibiting EEC are particularly extensive for nucleic acid complexes and because existing coarse{grained models of DNA allow us to explore the influence of changes in molecular parameters on the energetic parameters governing the stability of dsDNA by using molecular dynamics (MD) simulation. Since previous experimental and computational scientific works have suggested that changes in molecular rigidity or configurational entropy of the binding molecules are the primary cause of EEC, we estimate both measures of DNA molecular rigidity and configurational entropy under a wide range of conditions, along with resultant changes in the enthalpy and entropy of binding based on a two{state model of dsDNA melting. In particular, we consider variations in the rigidity and configurational entropy of dsDNA that arise from changing the associative interaction strength between the DNA bases, the length of the DNA chains, and the bending stiffness of the individual DNA chains (absorbing effects of hydration and paired counter-ions into the persistence length of our coarse{grained DNA model).

Citation

Soft Matter

Pub Type

Journals

Keywords

DNA, RNS, principles of molecular binding, entropy-enthalpy compensation, DNA melting, molecular rigidity, chain persistence length, Debye-Waller factor

Citation

Douglas, J. , Vargas-Lara, F. and Starr, F. (2017), Molecular Rigidity, Excess Entropy, and Enthalpy-Entropy Compensation in DNA Melting, Soft Matter (Accessed May 7, 2024)