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Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics.
- Source :
-
Journal of Chemical Physics . 9/7/2023, Vol. 159 Issue 9, p1-15. 15p. - Publication Year :
- 2023
-
Abstract
- DNA deformability and differential hydration are crucial determinants of biological processes ranging from genetic material packaging to gene expression; their associative details, however, remain inadequately understood. Herein, we report investigations of the dynamic and thermodynamic responses of the local hydration of a variety of base pair sequences. Leveraging in silico sampling and our in-house analyses, we first report the local conformational propensity of sequences that are either predisposed toward the canonical A- or B-conformations or are restrained to potential transitory pathways. It is observed that the transition from the unrestrained A-form to the B-form leads to lengthwise structural deformation. The insertion of intermittent -(CG)- base pairs in otherwise homogeneous -(AT)- sequences bears dynamical consequences for the vicinal hydration layer. Calculation of the excess (pair) entropy suggests substantially higher values of hydration water surrounding A conformations over the B- conformations. Applying the Rosenfeld approximation, we project that the diffusivity of water molecules proximal to canonical B conformation is least for the minor groove of the canonical B-conformation. We determine that structure, composition, and conformation specific groove dimension together influence the local hydration characteristics and, therefore, are expected to be important determinants of biological processes. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 00219606
- Volume :
- 159
- Issue :
- 9
- Database :
- Academic Search Index
- Journal :
- Journal of Chemical Physics
- Publication Type :
- Academic Journal
- Accession number :
- 171809433
- Full Text :
- https://doi.org/10.1063/5.0154977