Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature.

The validity of a theoretical nearest-neighbor model based on conformational energy calculations, for translating the deterministic fluctuations of DNA base sequences in superstructural elements, is tested on the electrophoretic data of 450 multimeric, duplex oligonucleotides with different sequence, periodicity, and complexity, corresponding to all the experimental data so far published. An accurate semiempirical linear relation between the gel electrophoretic retardation and the dispersion of the theoretical curvature was found which allows a prediction of electrophoretic anomalies of DNA tracts, e.g., the cyclic permutation gel assays, with great confidence. Such a pattern of agreement allows the interpretation of the gel electrophoresis retardation as due to an increase of activation energy required in straightening the DNA axis.