Abstract
As all the genetic information contained within DNA is buried within the duplex helix, there must be a series of breathing fluctuations that expose the nucleic bases to aid roles like replication, transcription, and repair. The work presented here uses a classical chromophore model under the point dipole approximation to calculate the circular dichroism as well as the absorption spectra of oligonucleotides at individual conformational states. This analysis will aid in the evaluation of these breathing fluctuations by treating systems of dimers and small length oligonucleotides as local models of these fluctuations.
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