Department of Genetics and Developmental Biology,1 Mary Babb Randolph Cancer Center,2 .... Mailing address: Mary Babb Randolph ...... Fields virology, vol.
Effect of Distance between Homologous Sequences and 3⬘ Homology on the Frequency of Retroviral Reverse Transcriptase Template Switching KRISTA A. DELVIKS1,2
AND
VINAY K. PATHAK2,3*
Department of Genetics and Developmental Biology,1 Mary Babb Randolph Cancer Center,2 and Department of Biochemistry,3 West Virginia University, Morgantown, West Virginia 26506 Received 11 March 1999/Accepted 17 June 1999
Deletion of direct repeats in retroviral genomes provides an in vivo system for analysis of reverse transcriptase (RT) template switching. The effect of distance between direct repeats on the rate of deletion was determined for 16 murine leukemia virus (MLV)-based vectors containing a 701-bp direct repeat of overlapping fragments of the herpes simplex virus thymidine kinase gene (HTK). The direct repeats were separated by spacer fragments of various lengths (0.1 to 3.5 kb). Southern analysis of infected cells after one replication cycle indicated that all vectors in which the distance between homologous sequences was >1,500 bp deleted at very high rates (>90%). In contrast, vectors containing
