Sliding clamps are ring-shaped proteins that encircle DNA and confer high processivity on DNA polymerases. Here we report the crystal structure of the five-protein clamp loader complex (replication factor-C, RFC) of the yeast Saccharomyces cerevisiae, bound to the sliding clamp (proliferating cell nuclear antigen, PCNA). Tight interfacial coordination of the ATP analogue ATP-gammaS by RFC results in a spiral arrangement of the ATPase domains of the clamp loader above the PCNA ring. Placement of a model for primed DNA within the central hole of PCNA reveals a striking correspondence between the RFC spiral and the grooves of the DNA double helix. This model, in which the clamp loader complex locks onto primed DNA in a screw-cap-like arrangement, provides a simple explanation for the process by which the engagement of primer-template junctions by the RFC:PCNA complex results in ATP hydrolysis and release of the sliding clamp on DNA.

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Apurinic/apyrimidinic (AP) sites are ubiquitous DNA lesions that are highly mutagenic and cytotoxic if not repaired. In addition, clusters of two or more abasic lesions within one to two turns of DNA, a hallmark of ionizing radiation, are repaired much less efficiently and thus present greater mutagenic potential. Abasic sites are chemically labile, but naked DNA containing them undergoes strand scission slowly with a half-life on the order of weeks. We find that independently generated AP sites within nucleosome core particles are highly destabilized, with strand scission occurring ∼60-fold more rapidly than in naked DNA. The majority of core particles containing single AP lesions accumulate DNA-protein cross-links, which persist following strand scission. The N-terminal region of histone protein H4 contributes significantly to DNA-protein crosslinks and strand scission when AP sites are produced approximately 1.5 helical turns from the nucleosome dyad, which is a known hot spot for nucleosomal DNA damage. Reaction rates for AP sites at two positions within this region differ by ∼4-fold. However, the strand scission of the slowest reacting AP site is accelerated when it is part of a repair resistant bistranded lesion composed of two AP sites, resulting in rapid formation of double strand breaks in high yields. Multiple lysine residues within a single H4 protein catalyze double strand cleavage through a mechanism believed to involve a templating effect. These results show that AP sites within the nucleosome produce significant amounts of DNA-protein cross-links and generate double strand breaks, the most deleterious form of DNA damage.chromatin | oxidative damage | histone modification E xogenously and endogenously produced agents continuously damage DNA. More than 70 types of damage have been identified, and significant effort is expended to determine which of these lesions are biologically important (1, 2). The apurinic/apyrimidinic (AP) site is a ubiquitous form of DNA damage that is produced in excess of 10,000 lesions per cell each day (3). This highly mutagenic lesion results from spontaneous hydrolysis of native and damaged nucleotides. AP sites are also formed as intermediates during base excision repair of alkylated and oxidized nucleotides and are themselves removed by multiple enzymatic pathways (4, 5). In mammalian cells incision of the AP's 5′-phosphate by Ape1, followed by excision of the resulting 5′-terminal 2′-deoxyribose phosphate by DNA polymerase β is the major pathway for removing the lesion. Redundant repair pathways are reflective of the high mutagenic potential and large quantities of AP produced and are indicative of their physiological significance. Mammalian cells lacking Ape1, the major base excision repair protein responsible for incising AP sites, are embryonic lethal (6). Recent observations reinforce the perception that AP sites are cytotoxic. For instance, formation of bursts of AP sites by the natural product leinamycin is postulated to be the source of this antitumor agent's cy...