SUNY at Albany
June 19-23, 2001
The Role of DNA Flexibility and Curvature in Protein Binding
DNA molecules are distorted when packaged in chromatin and in many regulatory complexes. In interactions lacking sequence-specific protein contacts, DNA flexibility may play a dominant role. When binding to a flat surface, a rigid molecule should have an advantage over a flexible one, because the latter must give up more chain entropy to bind to the rigid surface. However, when binding to a highly curved surface the flexible molecule should have the advantage. This reasoning suggests that there should be an optimal surface curvature for which flexibility matters little for binding affinity. We suggest that the optimum curvature may be near that of DNA in the nucleosome, accounting for the small variation of core histone affinity for different sequences. The method of DNA cyclization kinetics provides a general approach to determining the curvature and flexibility, both bending and torsional, of specific DNA sequences. We illustrate this principle by applying the method to the TATAAACGCC sequence motif found in DNA sequences that have relatively high affinity for core histones. Replacement of 30 bp of generic DNA by three 10-bp repeats of the motif in small cyclization constructs increases cyclization rates by two orders of magnitude. We document a 13¼ bend in the motif, and characterize the direction of curvature. The bending force constant is smaller by nearly two-fold and there is a 35% decrease in the twist modulus, relative to generic DNA. We also document the global structure and flexibility of sequences closely related to the Drew-Dickerson dodecamer, along with determination of the influence of methylation at CpG steps. Our results establish a protocol for determination of the ensemble-averaged global solution structure and mechanical properties of any ~10 bp DNA sequence element of interest, providing information complementary to that from NMR and crystallographic structural studies. Comparison of the nucleosome affinity of straight DNA molecules of varying stiffness should allow estimation of the optimal surface curvature for uniform packaging energy.
D. M. Crothers*, D. Nathan, M. Roychoudhury
Department of Chemistry, Yale University, New Haven, CT, U.S.A.