The goal of this pilot project is to develop and apply theoretical chemical methods of simulating the stable conformations of nanometer-sized DNA with PNA with and without single-base mismatches, and of double-stranded DNA/PNA with an alkanethiol monolayer. The simulation project is part of a pair of studies aimed at developing a DNA nanoarray chip to enhance the speed and lower the cost of analyzing for gene variations or patterns. The associated pilot project is experimental, with the goals of fabrication and detection of nanopattern DNA arrays. Simulating the underlying mechanism of molecular interactions is needed: (1) to understand the basic charge transport properties of DNA/PNA in an electrochemical environment, and (2) to predict the forces characteristic of single-base mismatches in DNA/PNA to interpret experimental atom force microscopic (AFM) measurements of the arrays. Three aspects of simulating the systems under consideration need to be addressed. First the stable conformations of DNA/PNA with and without DNA mismatches need to be examined. The replica exchange Monte Carlo (REMC) method is well suited to identifying multiple low-energy configurations of complex systems. Molecular dynamics (MD) simulation will also be employed to determine the mechanism of hybridization. The second aspect to be considered will go beyond electronic effects to include internal vibrations of individual molecules and tribological effects in MD simulations. This extension is necessary to account for effects arising from kinks and gauche defects on the interaction of DNA/PNA with an alkanethiol monolayer when the former is indented into the latter in the course of AFM measurements. A third aspect to be considered arises from the need to understand charge transport properties that govern DNA/PNA in an electrochemical environment. This task requires a combination of MD with a molecular orbital method. The fragment molecular orbital (FMO) method is applicable to very large systems. It will be incorporated into an MD algorithm to create a direct FMO MD routine that will be used to examine the underlying mechanism that accounts for the high sensitivity of electrochemical detection to single-base mismatches.
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