Accession Number:

ADA196668

Title:

Environmental Effects on Oligonucleotide Structure

Descriptive Note:

Annual rept. 1 Jun 1987-31 May 1988

Corporate Author:

WESLEYAN UNIV MIDDLETOWN CT HALL-ATWATER LABS

Personal Author(s):

Report Date:

1988-07-01

Pagination or Media Count:

7.0

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.

Subject Categories:

  • Biochemistry
  • Genetic Engineering and Molecular Biology
  • Organic Chemistry

Distribution Statement:

APPROVED FOR PUBLIC RELEASE