B-Deoxyribonucleic Acid Energy Band Gap Semi-empirical Computer Simulation: Progress Report

Abstract

DNA-the carrier of genetic information in all living species and the building block oflife, is often heralded as the cornerstone ofa new generation of electronic  devices because of its electronic properties. Its biological properties are largely becoming irrelevant because it is used as a basic material for nanostructures. The unique assenbly properties of DNA together with its unparalleled recognition, optical characteristics, stability and adaptabiliny suggest that DNA nay be
come one of the most imnportant species in the general area of molecular electronics. One existing medical application of DNA is the assembled microfabricated DNA chips which can be used to probe whether certain genetic codes are in a
given specimen of DNA. The DA structure is ideal for electron transfer since some of the electron orbitals belonging to the bases overlap quite well with each other along the axis of the DNA. Due to the variety of DNA sequences, layouts, and conditions, physical mechanism responsible for conduction remains unclear In this study. the energy band gaps and relative energies of the CG and AT base pairs of a double helix structure of B-DNA with 2'-endo sugar form and four CG and AT B-DNA sequences are being calculated using semi-empirical geometry optimization/Polak Ribiere algorithm, to investigate whether DNA behaves as an insulator; semicon ductor, or a superconductor, basing On the electron transfer theory. The calculated HOMO-LUMO difference signifies the energy band gap of the molecule. DNA consisting only of C and G bases is expected to conduct somewhat better than DNA with A and T bases or a poly (dG)-poly (dC) DNA is a large gap semi conductor (i.e. an 'insulator). The calculations are being performed using HyperChem suite of programs and utilizing Paranetric Method Number 3 (PM3). The conputations are being caried out on a Windows 2000 workstation in a
Pentiumn J|I PC.