We have examined the ability of singlestranded DNA to participate in homologous recombination reactions in mammalian cells and nuclear extracts derived from them. We have inserted a fragment of the neo gene into the single-stranded DNA phage vector M13 mphl. The neo fragment was derived from a deletion derivative of the prokaryotic-eukaryotic shuttle vector pSV2neo. The resulting singlestranded DNA was mixed with a double-stranded deletion derivative of pSV2neo and tested for recombination in human cells, monkey cells, and nuclear extracts obtained from human cells. We were able to obtain recombinant molecules containing wild-type neo genes in all three systems. Examination of the products of recombination indicated that they resulted from correction of the deletion in the double-stranded DNA substrate. We were unable to detect any extensive conversion of single-stranded DNA into its double-stranded counterpart before it participated in the recombination reaction. We have also tested the ability of single-stranded DNA to yield transfectants. When a single-stranded DNA derivative of the herpes simplex virus thymidine kinase (TK) gene was introduced into mouse L-M(TK-) cells, we were able to obtain TKV colonies.From these results, we conclude that single-stranded DNA can participate in transfection as well as homologous recombination reactions in mammalian cells.Integration of exogenous DNA into mammalian chromosomes by homologous recombination would be the preferred strategy for gene replacement therapy and in vivo gene modification. Mammalian somatic cells have been shown to contain all of the enzymes required to mediate recombination between homologous viral or plasmid sequences cotransfected into cells or between chromosomal sequences and their homologous counterparts (1-6). The exact nature of the proteins involved and the mechanism by which homologous recombination occurs in mammalian cells is not understood.We have developed a set of three systems to study the genetic and biochemical aspects of homologous recombination in mammalian cells (7-9). All of these involve the use of two derivatives of the prokaryotic-eukaryotic shuttle vector pSV2neo, a plasmid containing the bacterial gene for aminoglycoside 3'-phosphotransferase, which can be expressed in bacterial as well as in mammalian cells, resulting in neomycin or kanamycin resistance in bacteria and G418 resistance in mammalian cells. It also has an ampicillinresistance (AmpR) gene. Each of the two recombination substrates is a nonoverlapping, nonreverting deletion derivative of pSV2neo. The two deletion derivatives are referred to as pSV2neo DL and pSV2neo DR (7). In the first system, homologous recombination is studied by cotransfecting the two deletion plasmids into mammalian cells and selecting the cells for the expression of the normal neo gene, which can be generated by homologous recombination (7). The second method, somewhat analogous to studying bacteriophage recombination, involves introducing these substrates into monkey COS cells (10) ...