The Solution Structure of a Psoralen Cross-Linked DNA Duplex by NMR and Relaxation Matrix Refinement

Abstract

The three dimensional structure of the DNA oligomer d(5′-GGGTACCC-3′)2cross-linked with 4′-aminomethyl-4,5′,8-trimethylpsoralen(AMT) has been determined by two-dimensional NMR and a relaxation matrix refinement method. NMR data and structural calculation establish that the cross-linking of the psoralen in the B-DNA duplex retains Watson-Crick type hydrogen bonding throughout the duplex, although the thymine residue which is cross-linked with psoralen forms a weaker hydrogen bond. The psoralen cross-linking in DNA duplex induces significant change of the local DNA structure, but has no important effect on overall DNA helix. Our observation places an upper limit of 10° on overall DNA bending by psoralen cross-linking, which is consistent with the result of HMT-octamer cross link [Spielmann, H. P., Dwyer, T. J., Sastry, S. S., Hearst, J. E., and Wemmer, D. E., (1995)Proc. Natl. Acad. Sci. USA92,2345–2349] and gel electrophoretic study [Haran, T. E., and Crothers, D. E. (1988)Biochemistry27,6967–6971].