a DNase I cut site was incorrectly given as a 3' phosphate. The liberation of fragments with 3' hydroxyls by this enzyme makes the charge of these fragments the same as that of those liberated by T4 polymerase-exonuclease. The latter fragments differ only by the presence of a PD (cyclobutane pyrimidine dimer) at the 3' end.Proc. Natl. Acad. Sci. USA Vol. 84, pp. 6644-6648, October 1987 Biochemistry UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases (UV photoproduct ABSTRACTWe have determined the distribution of the major UV-induced photoproducts in nucleosome core DNA using the 3'-*5' exonuclease activity of T4 DNA polymerase, which has been shown to stop digestion immediately 3' to UV-induced pyrimidine dimers. This assay is extremely sensitive since all DNA fragments without photoproducts (background) are reduced to small oligonucleotides, which can be separated from those fragments containing photoproducts. The results show that the distribution of UV-induced photoproducts (primarily cyclobutane dipyrimidines) is not uniform throughout core DNA but displays a striking 10.3 (± 0.1) base periodicity. Furthermore, this characteristic distribution of photoproducts was obtained regardless of whether nucleosome core DNA was isolated from UV-irradiated intact chromatin fibers, histone H1-depleted chromatin fibers, isolated mononucleosomes, or cells in culture. The yield of pyrimidine dimers along the DNA seems to be modulated in a manner that reflects structural features of the nucleosome unit, possibly core histone-DNA interactions, since this pattern was not obtained for UV-irradiated core DNA either free in solution or bound tightly to calcium phosphate crystals. Based on their location relative to DNase I cutting sites, the sites of maximum pyrimidine dimer formation in core DNA mapped to positions where the phosphate backbone is farthest from the core histone surface. These results indicate that within the core region of nucleosomes, histone-DNA interactions significantly alter the quantum yield of cyclobutane dipyrimidines, possibly by restraining conformational changes in the DNA helix required for formation of these photoproducts.Irradiation by UV light produces a variety of lesions in cellular DNA, which, if unrepaired, may have lethal, mutagenic, or carcinogenic effects (1). The major lesion produced is the cyclobutane pyrimidine dimer (PD) formed between adjacent pyrimidines (2, 3), and the photochemistry of the formation of this lesion has been studied in detail (3). Several other photoproducts are also formed to a lesser extent. Among these are the pyrimidine-pyrimidone(6-4) adducts, which may play an important biological role since they have been shown to correlate with some mutational "hot spots" in specific DNA sequences (4).Since the "target" for PD formation in intact cells is DNA folded into the compact structure of chromatin (for reviews on chromatin structure, see refs. 5 and 6), it is important to understand the influence of...

We have compared the distributions of two stable UV photoproducts in nucleosome core DNA at the single-nucleotide level using a T4 polymerase-exonuclease mapping procedure. The distribution of pyrimidine-pyrimidone (6-4) dimers was uncovered by reversing the major UV photo-product, cis-syn cyclobutane pyrimidine dimer, with E. coli DNA photolyase and photoreactivating light. Whereas the distribution of total UV photoproducts in nucleosome core DNA forms a striking 10.3 base periodic pattern, the distribution of (6-4) dimers is much more random throughout the nucleosome core domain. Therefore, histone-DNA interactions in nucleosomes strongly modulate formation of the major class of UV-induced photoproducts, while having either a constant effect or no effect on (6-4) dimer formation.

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