Environmental Effects on Oligonucleotide Structure
Abstract
This project involves application of molecular simulation: molecular dynamics and Monte Carlo calculations to the structure, dynamics and solvation of oligonucleotide systems. Environmental effects are included in the simulations in a series of models involving progressively greater dimensionality, beginning with linear and sigmoidal forms of distance dependent dielectric functions representing the effect of water, and currently conventional screened charge models for the effect of counterions. The next level of rigor involves explicit consideration of oligonucleotide plus water with implicit (screened charge) counterion atmosphere and vice versa, explicit counterions with implicit (polarizable dielectric) water. Ultimately supercomputer simulations involving explicit representations of oligonucleotide, water and counterions will be studied, with special attention to the important but unexplored (and seemingly underappreciated) convergence issues in the calculations at this level. We hope to develop and characterize a protocol for optimum simulation methodology required to produce reliable, reproducible results. Detailed comparison of the nucleic acid dynamics for these different environmental models will be developed also in terms of conformational and helicoidal analysis. Hydration and counterion atmosphere will be analyzed based on stereographic display of solvation density and the systematic partitioning of the complex results into well-defined contributions from the major groove, minor groove and sugar-phosphate backbone entities of the duplex. Deoxyribonucleic acids.
Document Details
- Document Type
- Technical Report
- Publication Date
- Jul 01, 1988
- Accession Number
- ADA196668
Entities
People
- David L. Beveridge
Organizations
- Wesleyan University