Computational characterization of two lesions in DNA: 8-oxo-adenine and abasic site
EMSL Project ID
5119
Abstract
Effects of chemical modifications of nucleic acid bases on the structure and stability of DNA will be characterized through large scale computations. Initial molecular dynamics optimizations for normal DNA fragments (typically twelve pairs of nucleotides) will be followed by quantum mechanical structural optimizations of three or five pairs of nucleotides with chemically modified nucleic acid bases using the density functional level of theory (DFT) with the B3LYP exchange-correlation functional and 6-31G** basis sets. These DFT calculations extend to the nano scale and provide unique insight into the atomic and electronic structure of normal and modified DNA. In the current project we will concentrate on two lesions: 8-oxo-adenine and an abasic site (site with a missing base). The abasic site will be placed with either adenine or guanine or thymine or cytosine on the opposite strand. This research will provide a fundamental, quantitative, first-principles basis in DOE efforts to assess effects of radiation on DNA. These DFT calculations are performed with the NWChem software, a state-of-the-art computational chemistry package specifically designed for efficient execution on massively parallel computers.
Project Details
Project type
Capability Research
Start Date
2003-10-22
End Date
2004-11-15
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Abstract of paper presented at the 2020 virtual meeting on Epigenetics & Chromatin, September 15 - September 18, 2020
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