The solution structure of DNA decamer duplex containing the Dewar product of thymidylyl(3-->5')thymidine by NMR and full relaxation matrix refinement.

The (6-4) adducts and their Dewar isomers play an important role in cytotoxicity and mutation in skin cells exposed to sunlight. Structural study of the DNA duplex containing a site-specific photoproduct is an essential step toward understanding the molecular mechanism of the mutagenesis and the repair activity of UV-irradiated DNA. Here we use 1H NMR spectroscopy and full relaxation matrix refinement to investigate the solution structure of the duplex Dewar decamer. We find that the isomerization of the (6-4) adduct to its Dewar form induces a substantial change in overall structure of the oligonucleotide duplex. Contrasting base stacking of two lesion sites results in a large difference in the structural impacts induced by the two photoproducts, such as differential disruption of hydrogen bonding at the lesion sites and overall helical bending of 44 degrees by the (6-4) lesion and 21 degrees by the Dewar lesion.