Sequence Dependence of DNA Hypochromism

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Abstract
We report time dependent Hartree calculations of the hypochromism of mixed sequence DNA segments. Self-consistent field nucleotide wavefunctions are accurate enough to show some of the observed sequence dependence of DNA hypochromism. The results of time dependent Hartree theory are shown to be consistent with empirical sequence analyses that have been reported. On the basis of this consistency we can say that conclusions based on the empirical analyses are also well founded in theory. Specifically, (a) DNA hypochromism is not expected to have a simple linear dependence on AT content; (b) DNA's that have a random nearest neighbor frequency distribution will show a quadratic dependence of hypochromism on AT content which is approximately linear over any fairly large range of AT content; (c) past observations of near linearity for some DNA's were a direct consequence of those DNA's having a nearly random nearest neighbor frequency distribution; and (d) DNA's which deviate from the expected dependency have nonrandom nearest neighbor frequency distributions.