DNA bending and sequence-dependent backbone conformation - NMR and computer experiments

Although DNA bending plays a crucial role in several biological processes, very little is known experimentally about the relationship between sugar ph osphate conformation and sequence directed bending. In this paper, we deter mine the coupling constants for a nonselfcomplementary 11-mer A-tract DNA d uplex from 2D NMR experiments and along each chain of the duplex, we report the sugar pucker, torsional preferences and conformational averaging about the C3'-C3', C4'-C5' and C5'-O5' bonds for each nucleotide. The A-tract ex ists as an Equilibrium blend of canonical B-form and noncanonical B-form in which the exocyclic C4'-C5' bond is in trans conformation as in the origin al Watson-Crick model [Crick, F.H.C. & Watson, J.D. (1954) Proc. Roy. Soc. (London), A223, 80-96]. The trans conformation at the C4'-C5' can increase the interphosphate distance and lead to local unwinding of the duplex and r olling of the base pair into the major groove. This will create a kink or h inge. At the 3'-end of the A-tract in the purine-thymine step, the duplex i s compressed by the presence of a junction between A and B forms of DNA exc lusively in one strand, with consequent reduction of the phosphate-phosphat e distance. The coupling constant data seriously disagree with the A-tract DNA bending model of Crothers [Koo, H.-S., Wu, H.-M. & Crothers, D.M. (1986 ) Nature 320, 501-506], but is in agreement with the finding of Leroy et nl . [Leroy, J.-L., Charretier, E., Kochoyan, M. & Gueron, M. (1988) Biochemis try 27, 8894-8898] that the structure that drives bending in the A-tract is locally different from B-DNA. Structural distortions are extremely localiz ed with little or no propagation. It is likely that transcription factor pr oteins recognize these preexisting deformations in the free DNA itself and mold it into the matrix of the protein.