Psoralens are a class of photo-mutagenic and photo-chemotherapeutic molecules that covalently modify nucleic acids. They belong the family of small molecules that intercalate into and photoalkylate double stranded DNA. The primary target of psoralens are thymidine residues, and these molecules form both monoadducts and interstrand crosslinks. The reaction takes place between the 3,4 (pyrone) or 4',5' (furan) double bonds of the psoralen and the 5,6 double bond in pyrimidines .

      HMT, 4'-hydroxymethyl-4,5',8-trimethylpsoralen, 1 , is a synthetic psoralen and we have solved the structures of both the HMT furan-side monoadducted (MAf) and interstrand crosslinked (XL) dsDNA molecules have been determined by NMR spectroscopy and restrained molecular dynamics. The three-dimensional structure of the MAf and photoisomeric XL show that the conformational differences between undamaged DNA and the adducted molecules are localized to within three basepairs of the damage.

      Psoralen damaged DNA is recognized by both the human repair system and the prokaryotic (A)BC excinuclease and serves as an excellent model to study the structural and dynamic motifs that cellular repair enzyme systems may recognize. Results from the 1H NMR experiments on the MAf and XL suggest that damage results in conformational heterogeneity for the near by sugar residue. These results suggest that characterization of the changes in nucleic acid dynamics may be important for understanding DNA damage and repair. Comparisons of the structural and dynamic differences between the UM and the MAf allow for examination of features that may be recognized by the enzyme system. Understanding how the NER excinuclease recognizes psoralen damage to DNA will assist in the elucidation of the general mechanism of lesion recognition. The photobinding of HMT to dsDNA results in substantial structural distortion to the normal B-form DNA helix. This distortion is hypothesized to be responsible for changes in the DNA structure that allow for the recognition of the damage by the nucleotide excision repair system. Direct recognition of the HMT lesion by the repair proteins is unlikely because a wide variety of DNA lesions that do not share common structural features are recognized and removed from DNA by NER. A proposed mechanism for the recognition of damage by NER involves the recognition of altered backbone conformations that are only accessible to damaged DNA and not normal DNA.

We have studied the dynamics of undamaged (UM) and HMT monoadducted (MAf) DNA oligomer d(GCGTACGC)2 based on 13C relaxation measurements made by using proton detected 13C-1H 2D NMR spectroscopy. This study forms the background for a comparative analysis with other types of DNA damage that is recognized by the NER system. These comparisons will provide detailed information on the changes in structure and dynamics that occur as a result of damage to the DNA helix and will suggest mechanisms used for recognition of this damage by repair systems.