Isolation and characterization of recombinant DNA clones of avian retroviruses: size heterogeneity and instability of the direct repeat.

Unintegrated proviral DNA of Schmidt-Ruppin B Rous sarcoma virus was cloned in the bacteriophage lambda vector Charon 21A. A total of 12 independent recombinant lambda SRBtd clones which were derived from the transformation-defective component in the viral preparation were analyzed with restriction endonucleases and molecular hybridization techniques. Three classes of clones were observed. Type I clones contained a 5.0-megadalton insert of viral DNA, type II clones contained phage with two size classes of inserts (5.0 and 5.2 megadaltons), and one type III clone contained only a 5.2-megadalton insert. The smaller insert present in type II clones appeared to be derived by deletion of one copy of a directly repeated sequence which was present in the larger insert. Mapping data indicated that the deletion includes all or part of the terminal repeat found in linear double-stranded proviral DNA. Similar results were obtained from lambda RAV2 recombinant clones derived from Rous-associated virus type 2. Analysis of DNA from type II and type III clones of lambda SRBtd and lambda RAV2 revealed limited heterogeneity in the size of the direct repeat.