The relative biological importance of cis-syn cyclobutane dimer and pyrimidine(6–4)pyr-imidone photoadduct ([6–4] photoadduct) appears to be dependent on the biological species, dipyrimidine sites and the local conformational variation induced at the damaged sites. The single-stranded deoxyn-ucleotide 10-mers containing the site-specific (6–4) adduct or cis-syn cyclobutane dimer of thymidylyl (3'-5')-thymidine were generated by direct photolysis of d(CGCATTACGC) with UVC (220–260 nm) irradiation or UVB (260–320 nm) photosensitization. Three-dimensional structures of the duplex cis-syn and (6–4) decamers of d(CGCATTACGC)d(GCGTAATGCG) were determined by NMR spectroscopy and the relaxation matrix refinement method. The NMR data and structural calculations establish that Watson-Crick base pairing is still intact at the cis-syn dimer site while the hydrogen bonding is absent at the 3'-side of the (6–4) lesion where the T [RIGHTWARDS ARROW] C transition mutation is predominantly targeted. Overall conformation of the duplex cis-syn decamer was B-DNA and produced a 9° bending in the DNA helix, but a distinctive base orientation of the (6–4) lesion provided a structural basis leading to 44° helical bending. The observed local structure and conformational rigidity at the (6–4) adduct of the thymidylyl(3'-5')-thymidine (T-T [6–4]) lesion site suggest the potential absence of hydrogen bonding at the 3' sides of the (6–4) lesion with a substituted nucleotide during replication under SOS conditions. Contrasting structural distortions induced by the T-T (6–4) adduct with respect to the T-T cis-syn cyclobutane pyrimidine photodimer may explain the large differences in mutation spectrum and repair activities between them.