WebSIDD: Server for predicting stress-induced duplex destablized (SIDD) sites in superhelical DNA

Abstract

Summary: WebSIDD is a Web-base service designed to predict locations and extents of stress-induced duplex destabilization (SIDD) that occur in a double-stranded DNA molecule of specified base sequence, on which a specified level of superhelical stress is imposed. The algorithm calculates the approximate equilibrium statistical mechanical distribution of a population of identical molecules among its accessible states. The user inputs the DNA sequence, and the program outputs the calculated transition probability and destabilization energy of each base pair in the sequence. As options, the user can specify the temperature and the level of superhelicity. The values of all structural and energy parameters used in the calculation have been experimentally measured. WebSIDD should prove useful for finding SIDD-susceptible sites in genomic sequences, and correlating their occurrence with locations involved in regulatory and pathological processes. This strategy already has illuminated the roles of SIDD in diverse biological regulatory processes, including transcriptional initiation and termination, and the eukaryotic nuclear scaffold attachments that partition chromosomes into domains. © Oxford University Press 2004; all rights reserved.