Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption
and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models,
molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from
simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded
solvent molecules were simulated on the basis of density-functional calculations on small fragments and
subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared.
Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal
base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum
for (CG)2 nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the
molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully
reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained
for the dependence on the basis sequence.