CURVATURE: software for the analysis of curved DNA

Software is presented to plot the sequence-dependent spatialtrajectory of the DNA double helix and/or distribution of curvaturealong the DNA molecule. The nearest-neighbor wedge model isimplemented to calculate overall DNA path using local helixparameters: helix twist angle, wedge (deflection) angle anddirection (of deflection) angle. The procedures described provedto be very convenient as tools for investigation of a relationshipbetween overall DNA curvature and its gel electrophoretic mobility.All parameters of the model had been estimated from experimentaldata. Using these wedge parameters the program takes, as input,any DNA sequence and calculates the likely degree of curvatureat each point along the molecule. This information is displayedboth graphically and in the form of simplified representationsof curved double helices. The Software, CURVATURE, can thusbe used to investigate possible roles of curvature in modulationof gene expression and for location of curved portions of DNA,which may play an important role in sequence-specific protein-DNAinteractions.