Access to the genetic code requires severe changes in local DNA structure. Proteins usually gain access to the atoms holding the code by a partial unwinding and bending of the double helix, processes that can give rise in the DNA to ``supercoiling'' (Bauer et al., 1980). Deciphering the sequence-dependent structural and deformational codes in DNA as well as the interplay between the local and long-range structure associated with its biological activity require a variety of mathematical and computational approaches: tools to extract knowledge-based ``energies'' from structural and thermodynamic nucleic acid databases, such as those organized at Rutgers (Berman et al., 1992); techniques to simulate the dynamical structures and equilibrium properties of ensembles of DNA molecules, (Beveridge, 1998; Jian et al., 1998); explicit and exact solutions of the non-linear equations governing the supercoiled shapes of a deformable DNA elastic rod (Goldstein et al., 1998; Swigon et al., 1998); analysis of the topological forms of DNA produced by enzymatic action (Crisona et al., 1999); explicit expressions to incorporate base sequence-dependent structural information in genomic analyses, (Sheridan et al., 1998; Yeramian, 1999).
This workshop will bring together such diverse perspectives on DNA topology to build bridges not only between mathematics and molecular biology but also between the mathematical and physical scientists currently focused on either the local or global view of DNA structure. This workshop follows two previous DIMACS workshops on DNA topology. Those dealt exclusively with the global folding of idealized, sequence-independent DNA rods and made no connection to the structural and energetic information embedded in the genetic code. The databases of DNA 3D structures have grown to the point where only now is it possible to extract the sequence-dependent information required to connect macromolecular structure and properties to the sequence of DNA base pairs, making this workshop extremely timely.
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