A neighbor-interaction analysis of the hypochromism and spectra of DNA.

A mathematical method has been developed for analysis of the spectral changes associated with the helix → coil and helix → nucleotide transitions of DNA. The method depends upon a model in which hypochromism arises from the interaction of base pairs along the helix. It is shown that if the distribution of base pairs is random, the dependence of hypochromism upon base composition is quadratic, taking into account the pairwise interactions between each base pair and all others on the helix, no matter how far away. Two methods of analyzing thermal denaturation data by this method are given; either one leads to precise determination of the composition of the denaturing regions, and a crude measure of deviations of nucleotide sequences from randomness. One of these methods also leads to an explanation of the effectiveness of this and earlier methods in analyzing denaturation. Spectral data have been obtained for a large number of bacterial DNA's for evaluation of the necessary parameters in the new equations. It is shown that the helix → coil transition data are approximated reasonably well at most wavelengths by a linear equation (i.e. the quadratic term is small), but that the helix → nucleotide and coil → nucleotide data are not. The quadratic dependence upon base composition of helix → nucleotide and coil → nucleotide spectral changes indicates that the spectra of the helix and of fully denatured DNA are sensitive to the distribution of neighbors around each base pair. The new methods of spectral analysis may also be adapted readily for the determination of the base composition, concentration and extent of denaturation of an unknown DNA sample.