The repair of 12-, 27-, 62-, and 216-nucleotide unpaired insertion/deletion heterologies has been demonstrated in nuclear extracts of human cells. When present in covalently closed circular heteroduplexes or heteroduplexes containing a single-strand break 3 to the heterology, such structures are subject to a low level repair reaction that occurs with little strand bias. However, the presence of a single-strand break 5 to the insertion/ deletion heterology greatly increases the efficiency of rectification and directs repair to the incised DNA strand. Because nick direction of repair is independent of the strand in which a particular heterology is placed, the observed strand bias is not due to asymmetry imposed on the heteroduplex by the extrahelical DNA segment. Strand-specific repair by this system requires ATP and the four dNTPs and is inhibited by aphidicolin. Repair is independent of the mismatch repair proteins MSH2, MSH6, MLH1, and PMS2 and occurs by a mechanism that is distinct from that of the conventional mismatch repair system. Large heterology repair in nuclear extracts of human cells is also independent of the XPF gene product, and extracts of Chinese hamster ovary cells deficient in the ERCC1 and ERCC4 gene products also support the reaction.Base pairing anomalies can occur within the DNA helix as a consequence of DNA biosynthetic errors or as a result of recombinational strand transfer between sequences that differ genetically (1-4). Such pairing errors may take the form of base-base mismatches or insertion/deletion (I/D) 1 heterologies, in which one strand contains a segment of one or more unpaired nucleotides. Strand-specific correction of base-base and I/D mismatches produced during DNA biosynthesis plays an important role in mutation avoidance (2, 5, 6), and mismatch rectification within the recombination heteroduplex has been implicated in meiotic gene conversion in fungal systems (3,4,7,8).Base-base mispairs are subject to strand-specific correction by the mismatch repair systems of both prokaryotes and eukaryotes (5, 6, 9), but action of this system on I/D mismatches is limited to fairly small heterologies. The Escherichia coli mismatch repair pathway will correct I/D heterologies up to about 7 unpaired nucleotides, but larger heterologies are poorly processed by this system (10 -13). A similar specificity is characteristic of the human mismatch repair system, which can correct I/D heterologies up to about 8 unpaired nucleotides (14 -16).There is evidence, in some cases contradictory, that both prokaryotes and eukaryotes can rectify I/D heterologies with larger unpaired segments by a pathway distinct from the mismatch repair system. Using transfection assay, Dohet et al. (10) demonstrated rectification of a bacteriophage heteroduplex containing an 800-nucleotide unpaired IS1 heterology by a pathway that was independent of mutH, mutL, and mutS gene function. In contrast, Carraway and Marinus (12) failed to detect repair of large heterologies upon transformation of covalently closed circular ...