The trans-syn-I thymine dimer bends DNA by approximately 22 degrees and unwinds DNA by approximately 15 degrees

Irradiation of DNA with ultraviolet light leads to the formation of two classes of cyclobutane dimers at adjacent thymines sites, of which the cis-syn is the major class and the trans-syn is the minor class. While the structure and properties of DNA containing cis-syn thymine dimers have been extensively studied, virtually nothing is known about DNA containing trans-syn thymine dimers. To investigate the bending and unwinding of DNA induced by the trans-syn-I thymine dimer, the electrophoretic properties of oligomers of trans-syn-I dimer-containing DNA duplexes were studied. Oligonucleotides 10, 11, and 12 bp in length containing a centrally located trans-syn-I thymine dimer were synthesized, polymerized, and analyzed by polyacrylamide gel electrophoresis. In contrast to the small bending angle (approximately 7 degrees) induced by the cis-syn thymine dimer, we found that trans-syn-I thymine dimer bends DNA significantly (approximately 22 degrees). Both dimers, however, are found to unwind DNA by the same amount (approximately 15 degrees). On the basis of previous NMR studies, it appears that the bend of the trans-syn-I dimer is localized at the 5'-side of the dimer. Gel electrophoretic analysis of multimers of two 11-mers containing a cis-syn thymine dimer at the 5'-end and at the center of a dT6.dA6 tract confirmed our previous estimates for the bending angles of thymine dimer-containing T6 tracts. The substrates reported may be useful in determining how general repair enzymes recognize DNA damage.