Experimental evaluation of the Liu-Beveridge dinucleotide step model of DNA structure

Methods for predicting DNA curvature have many possible applications. Dinuc leotide step models describe DNA shape by characterization of helical twist , deflection angles and the direction of deflection for nearest neighbor ba se pairs. Liu and Beveridge have extended previous applications of dinucleo tide step models with the development and qualitative validation of a predi ctive method for sequence-dependent DNA curvature (the LB model). We tested whether the LB model accurately predicts experimentally deduced curvature angles and helical repeat parameters for DNA sequences not in its training set, particularly when challenged with quantitative data and subtle sequenc e phasings. We examined a series of 17 well-characterized DNA sequences to compare electrophoretic and computational results. The LB model is superior to two other models in the prediction of helical repeat parameters. We obs erved a strong linear correlation between curvature magnitudes predicted us ing the LB model and those determined by electrophoretic ligation ladder ex periments, although the LB model somewhat underestimated apparent curvature . With longer electrophoretic phasing probes the LB model slightly overesti mated gel mobility anomalies, with modest deviations in predicted helical r epeat parameters. Overall, our analyses suggest that the LB model provides reasonably accurate predictions for the electrophoretic behavior of DNA.