A 32-base-pair DNA fragment containing a thymine photodimer was constructed and ligated head-to-tail to obtain multimers of this sequence in which thymine dimers were in phase with the helix screw axis (=w3 turns apart). The ligation products were analyzed by one-and two-dimensional gel electrophoresis and quantitative electron microscopy. These analyses show that the thymine photodimer introduces a bend of =:30 in DNA, which causes anomalously slow migration of DNA fragments in polyacrylamide gels and facilitates the formation of small covalent circles. Repair of thymine dimers by DNA photolyase abolishes the anomalous migration.UV-induced pyrimidine dimers are perhaps the most frequent damage inflicted on DNA by the environment. The dimers are recognized and repaired by a number of enzymes, which use dissimilar chemical strategies (1, 2). To better understand the mechanism of dimer-induced mutation and cell lethality and how dimers are recognized by repair enzymes it will be necessary to know how the structure of DNA is altered by dimer or by other nucleotide diadducts that have similar biological effects. X-ray crystallography has been useful in determining the structures of pyrimidine dimer, psoralen, and cisplatin adducts in dinucleotide forms (3-5). However, it has not been possible so far to solve structures of oligonucleotides containing these adducts for lack of suitable crystals. Other methods such as melting temperature determinations (6), analysis of randomly damaged DNA on band-counting gels (7), molecular graphics based on energy minimization combined with model building (8, 9), and more recently two-dimensional NMR studies with a dimer-containing dodecanucleotide (10) have provided some useful, but at times contradictory, information regarding the structure of dimer-containing DNA.In this communication, we report the results of our studies on structural changes induced in DNA by a thymine dimer. For these studies, we have used a synthetic DNA fragment containing a thymine dimer at a unique location. This fragment was ligated in such a way that the multimers of the fragment contained thymine dimers at 32-base-pair (bp) intervals (-3 turns). The ligation products were then analyzed by gel electrophoresis and electron microscopy to detect structural anomalies-mainly bends or kinks.MATERIALS AND METHODS Materials. A synthetic 48-mer duplex with or without a thymine dimer was constructed by ligating 6 complementary oligonucleotides ranging in size from 11 to 17 nucleotides; the central 11-mer contained a cis,syn thymine dimer in one case and normal bases in the other. These 11-mers were labeled with 32P using polynucleotide kinase and therefore the resulting 48-mers contained internal labels. The construction and purification of the duplexes has been described elsewhere in detail (11), the only difference here being that "arm" oligomers of different sequences and lengths were used to construct BamHI and Bgl II sites on either sides of the dimer (or TT sequence) for eventual production of multim...