Molecular Modeling as a visualization tool in design of DNA crosslinked polyacrylamide

Abstract

Since DNA-crosslinked gels are likely to find a range of applications it is important to know how to tailor the gel composition for a particular application. In this study, polyacrylamide gel crosslinked with DNA has been assayed with respect to conformational energy and linker size using AMBER 7.0 software [1]. The molecular models generated in AMBER make it possible to estimate the mechanical properties of the gel as a function of crosslinker density, polyacrylamide density, and crosslinker length. The structure of an equilibrium state is computed using an explicitly solvated model, in which water was the solvent Visual inspection of the model determines other mechanical properties of the gel and helps predict chemical interactions. A long-term goal of this work is to use computer assisted modeling techniques to guide the experiments, to predict linker stiffness, and to examine other mechanical properties of the DNA crosslinker.