We have constructed simian virus 40 minireplicons containing uniquely placed cis,syn-thymine dimers (T< >T) for the analysis of leading-and lagging-strand bypass replication. Assaying for replication in a human cellfree extract through the analysis of full-size labeled product molecules and restriction fragments spanning the T< >T site resulted in the following findings: (i) Despite these investigations, a basic understanding of replication of damaged DNA in normal human cells is lacking (2).In vitro studies using primed single-stranded DNA templates and purified DNA polymerases (9-13) have demonstrated the existence of both stalled replication intermediates and translesion synthesis. These studies involved DNA synthesis on primed templates rather than semiconservative coordinated replication of leading and lagging strands at a bona fideThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. replication fork. In vitro replication of SV40-based minireplicons carrying randomly distributed, UVC-induced Pyr<>Pyr has been analyzed in human cell extracts (14,15). A UV fluence-dependent inhibition of covalently closed circular DNA (form I DNA) synthesis was observed, which confirmed the blocking effect of such lesions on DNA replication. The presence of a UV endonuclease V from phage T4 (T4 UV endo)-sensitive product implied that replication of Pyr<>Pyr occurred in such a system. A detailed examination of the molecular mechanism of UV damage processing has become possible with the development of site-specific lesioncontaining DNA (11-13). Thus, we now report sites of blockage and rates of bypass of individual lesions in the leading and lagging strands.The most prevalent DNA modification resulting from UVC irradiation is the cis,syn-thymine dimer (T<>T), which has been a paradigm DNA lesion (16). We have prepared plasmids containing the SV40 origin of replication together with uniquely placed T<>T and have analyzed their in vitro replication in a human cell-free extract. We have developed these assays to study the mechanism of replication of DNA damaged in either the leading or lagging strands of a human replication fork. Specifically, we have determined the site of blockage of strand elongation on T<>T-containing DNA templates, compared the bypass of T<>T in the leading and lagging strands, and analyzed the potential uncoupling of coordinated leading-and lagging-strand synthesis at T<>T-blocked replication forks. MATERIALS AND METHODS

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The B-lymphotrophic human herpes Epstein-Barr virus (EBV) is a 160-kilobase double-stranded DNA episomal virus carried in a persistent asymptomatic state by more than 90% of the worldwide adult population. We engineered a helper-dependent mini-EBV, with the minimal cis-EBV elements for episomal replication, viral amplification and packaging, for use as a gene delivery system. The therapeutic potential of this system was established by stably transducing B-lymphoblastoid cells from a Fanconi anaemia group C (FA-C) patient with a mini-EBV constitutively expressing the normal FACC cDNA and showing in vitro correction of the FA phenotype. In the absence of selective pressure, episomal expression persisted with a half-life of 30 days in actively growing transduced cells, indicating a retention rate of 98% expression per cell doubling. This work demonstrates the generation of an infectious non-transforming viral vector that can potentially deliver large therapeutic genes efficiently and selectively into human B cells.

We have developed a human artificial episomal chromosome (HAEC) system, based on the latent replication origin of the large herpes Epstein-Barr virus, for the propagation and stable maintenance of DNA as circular minichromosomes in human cells. Individual HAECs carried human genomic inserts ranging from 60-330 kb and appeared genetically stable. An HAEC library of 1,500 independent clones carrying random human genomic fragments with average sizes of 150-200 kb was established and allowed recovery of the HAEC DNA. Our autologous HAEC system, with human DNA cloned directly in human cells, provides an important tool for functional study of large mammalian DNA regions and gene therapy.

A novel shuttle vector, pBH140, has been constructed that allows stable maintenance of large genomic inserts as human artificial episomal chromosomes (HAECs) in mammalian cells. The vector, essentially a hybrid BAC-HAEC, contains an F-based replication system as in a bacterial artificial chromosome (BAC) and the Epstein-Barr virus (EBV) latent origin of replication system, oriP, for replication in human cells. A 185-kb DNA insert containing the entire human beta-globin locus, including its locus control region (LCR), was retrofitted into this vector. The resulting beta-globin BAC-HAEC clone, p148BH, was transfected into human cells and analyzed for episomal maintenance and expression of the beta-globin gene. FISH revealed an association of the vector with different human chromosomes but no integration. The beta-globin BAC-HAECs were present at an average copy number of 11-15 per nucleus in the stably transformed human cells. After 1 year of continuous in vitro cultivation, the HAECs persisted as structurally intact 200-kb episomes. While no beta-globin transcription could be detected in the parental D98/Raji cells, correctly spliced RT-PCR products were produced at significant levels in long-term cultures of the BAC-HAEC-transduced cells. The wide availability of BAC and PAC libraries, the ease in manipulating cloned DNA in bacteria, and the episomal stability of the pBH140 vector make this system ideal for studies on gene expression and other genomic functions in human cells. The potential significance of large, functionally active episomes for gene therapy is discussed.

We have developed a general quantitative method for comparing the levels of drug-induced DNA crosslinking in specific mammalian genes. We observed a dramatic difference between the efficiency of the removal of both psoralen monoadducts and interstrand crosslinks from the rRNA genes and the efficiency of their removal from the dihydrofolate reductase (DHFR) gene in cultured human and hamster cells. While 90% of the interstrand crosslinks were removed from the human DHFR gene in 48 h, less than 25% repair occurred in the rRNA genes. Similarly, in Chinese hamster ovary cells, 85% repair of interstrand crosslinks occurred within 8 h in the DHFR gene versus only 20% repair in the rRNA genes. The preferential repair of the DHFR gene relative to that of the rRNA genes was also observed for psoralen monoadducts in cells from both mammalian species. In human-mouse hybrid cells, the active mouse rRNA genes were five times more susceptible to psoralen modification than are the silent rRNA human genes, but adduct removal was similarly inefficient for both classes. We conclude that the repair of chemical damage such as psoralen photoadducts in an expressed mammalian gene may depend upon the class of transcription to which it belongs.

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We describe the microcell fusion transfer of 100-200 kb self-replicating circular human minichromosomes from human into mouse cells. This experimental approach is illustrated through the shutting of the latent 170 kb double-stranded DNA genome from the human herpesvirus, Epstein-Barr virus, into nonpermissive rodent cells. Using this interspecies transfer strategy, circular episomes carrying 95-105 kb of human DNA were successfully established at low copy number in mouse A9 cells. Selected episomes were stably maintained for 6 months, and unselected episomes were characterized by a 95% episomal retention per cell division. The establishment of a mouse artificial episomal chromosome system should facilitate evolutionary and therapeutic studies of large human DNA in rodent genetic backgrounds.