Structural studies of the photochemically damaged nucleic acid by NMR and molecular modeling

Abstract

Structural studies of the DNA duplex containing a site specific-photodamaged photoproduct is an essential step toward understanding the molecular mechanism of the mutagenesis and the repair activity of ultraviolet irradiated DNA. The solution structures of two photodamaged DNA, psoralen cross-linked octamer duplex and (6-4) adduct- and Dewar photoproduct- containing decamer duplex, have been elucidated by detailed NMR and molecular modeling. (1) The three dimensional structure of the DNA oligomer $d(5``-GGGTACCC-3``)_2$ cross-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. (2) The relative biological importance of (6-4) adduct and Dewar photoproduct appears to be dependent on the biological species, dipyrimidine sites, and the local conformational variation induced at the damaged sites. The single- stranded deoxynucleotide 10-mers containing site-specific (6-4) adduct or Dewar photoproduct of thymidylyl (3→5)-thymidine were generated by direct photolysis of d(CGCATTACGC) with UV-C(220-260nm) and UV-B(260-320nm) irradiation. Three-dimensional structures of the duplex Dewar and (6-4) decamers of d(CGCATTACGC)(d(GCGTAATGCG) were determined by NMR spectroscopy and relaxation matrix refinement method. NMR data and structural calculation establish that the hydrogen bonding is absent at the 3``-side of the (6-4) l...