A New “Dimension” to DNA Sequence Analysis

In addition to the genetic message, DNA base sequence carries structural and energetic signals that are related to its biological function. We have extracted “knowledge-based” energy functions from high-resolution crystal structures to study the sequence-dependent recognition and folding of the long, threadlike molecule. The deformations of individual base-pair steps are described by six independent “step” parameters: three angular variables (Tilt, Roll, Twist) and three variables (Shift, Slide, Rise) with dimensions of distance. The talk will focus on sequence contexts which underlie the looping of DNA which is implicated in its biological processing and packaging.