CURVATURE - SOFTWARE FOR THE ANALYSIS OF CURVED DNA

Software is presented to plot the sequence-dependent spatial trajector y of the DNA double helix and/or distribution of curvature along the D NA molecule. The nearest-neighbor wedge model is implemented to calcul ate overall DNA path using local helix parameters: helix twist angle, wedge (deflection) angle and direction (of deflection) angle. The proc edures described proved to be very convenient as tools for investigati on of a relationship between overall DNA curvature and its gel electro phoretic mobility. All parameters of the model had been estimated from experimental data. Using these wedge parameters the program takes, as input, any DNA sequence and calculates the likely degree of curvature at each point along the molecule. This information is displayed both graphically and in the form of simplified representations of curved do uble helices. The Software, CURVATURE, can thus be used to investigate possible roles of curvature in modulation of gene expression and for location of curved portions of DNA, which may play an important role i n sequence-specific protein - DNA interactions.