Electronic excitations and spectra in single-stranded DNA

Using density functional theory and molecular dynamics simulations, we show that delocalized states extending over three bases can be directly excited in single-stranded poly(A) DNA. The results are in semiquantitative agreement with recent experimental results for the delocalization length of these states in single- and double-stranded DNA. The structures used in these molecular dynamics calculations are validated by comparing calculated circular dichroic spectra for d(A)2 and d(A)4 with experiment. These spectra, which arise from highly stacked structures, are in good agreement with experiment, suggesting that the short delocalization in ssDNA arises in spite of strong stacking.