Excited states of DNA hairpins

EMSL Project ID

22990

Award DOI

https://dx.doi.org/10.46936/genr.proj.2006.22990/60003034

Abstract

We propose to investigate theoretically, using time-dependent density functional
methods, the excited states of DNA oligomeric structures (hairpins and
dumbbells) constituted of 1 to 6 base pairs. This presents a unique opportunity
in DNA excited states since these structures are produced routinely by
experimentalists at Northwestern University, and experimental data are
available on their UV and circular dichroism spectra. Gathering theoretical
data on the structure (partially already accomplished by our group in the
past two years) and spectra of these oligomers would be very fruitful and explain, in a controlled
environment, the effects of structural changes on the DNA excitations.
Comparing first principles calculations with state of the art experiments for
systems where both can be performed could elucidate trends that are impossible
both to detect experimentally and to model in large DNA strands, due to size and
structural complexity.
We have chosen the Molecular Science Computing Facility at PNNL as the site for this project
because it has already the specific software that we need for this research
(the density functional package ADF).
Due to an ongoing software development effort that our group has with ADF, this development effort
will eventually lead to enhancements in the version of ADF that is at PNNL as
well.