LTR-directed homologous recombination of full-length HIV-1 provirus clone in recA(-) bacteria.

During molecular cloning of full-length retroviral plasmid clones occurrence of homologous recombination (HR) between LTR regions is frequently observed. In order to evaluate appropriate host bacterial strains for cloning such HR-prone plasmids, we utilized a linearized template plasmid containing a full-length HIV-1 proviral sequence. The plasmid was linearized within the viral sequence so that plasmid transformed bacteria would grow only when the plasmid was circularized by HR. Using this genetic system for detecting HR, we evaluated the frequency of HR in various recA(-) bacterial strains which are commercially available and in some recA-null strains in which recA-defective phenotype was constructed by P1 transduction. We found that HR occurred even in recA-null strains although in lesser frequencies. The nucleotide sequence analysis at the junction of recombination revealed no loss, insertion or duplication of DNA sequence. It is suggested that recombination machinery other than the RecA system is involved.