AVIAN RETROVIRUS U3 AND U5 DNA INVERTED REPEATS - ROLE OF NONSYMMETRICAL NUCLEOTIDES IN PROMOTING FULL-SITE INTEGRATION BY PURIFIED VIRION AND BACTERIAL RECOMBINANT INTEGRASES

The U3 and U5 termini of linear retrovirus DNA contain imperfect inver ted repeats that are necessary for the concerted insertion of the term ini into the host chromosome by viral integrase. Avian myeloblastosis virus integrase can efficiently insert the termini of retrovirus-like DNA donor substrates (480 base pairs) by a concerted mechanism (full-s ite reaction) into circular target DNA in vitro. The specific activiti es of virion-derived avian myeloblastosis virus integrase and bacteria l recombinant Rous sarcoma virus (Prague A strain) integrase (similar to 50 nM or less) appear similar upon catalyzing the full-site reactio n with 3'-OH recessed wild type or mutant donor substrates, We examine d the role of the three nonsymmetrical nucleotides located at the 5th, 8th, and 12th positions in the U3 and U5 15-base pair inverted repeat s for their ability to modify the full-site and simultaneously, the ha lf-site strand transfer reactions. Our data suggest that the nucleotid e at the 5th position appears to be responsible for the 3-5-fold prefe rence for wild type U3 ends over wild type U5 ends by integrase for co ncerted integration. Additional mutations at the 5th or 6th position, or both, of U3 or U5 termini significantly increased (similar to 3 fol d) the full-site reactions of mutant donors over wild type donors.