The trans-syn-I Thymine Dimer Bends DNA by ≈22° and Unwinds DNA by ≈15°

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 (≈7°) induced by the cis-syn thymine dimer, we found that trans-syn-I thymine dimer bends DNA significantly (≈22°). Both dimers, however, are found to unwind DNA by the same amount (≈15°). 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.