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Integrase of the human immunodeficiency virus type-1 (HIV-1) recognizes specific sequences located in the U3 and U5 regions at the ends of viral DNA. We synthesizedDNA duplexes mimicking the U5 region and containing either 2¢-aminonucleosides or non-nucleoside 1,3-propanediol insertions at the third and terminal positions and studied their interactions with HIV-1 integrase. Both modifications introduced a local structural distortion in the DNA double helix. | Eur. J. Biochem. 271 205-211 2004 FEBS 2003 doi 10.1046 j.1432-1033.2003.03921.x HIV-1 integrase can process a 3 -end crosslinked substrate Implications of DNA end-fraying requirement during the 3 -processing reaction Julia Agapkina1 Maksim Smolov2 Evgeni Zubin2 Jean-Francois Mouscadet3 and Marina Gottikh2 Institute of the Chemical Physics Problems Russian Academy of Sciences Chernogolovka Russia 2Belozersky Institute of Physico-Chemical Biology and Chemical Department Lomonosov Moscow State University Moscow Russia 3LBPA CNRS UMR 8113 Ecole Normale Superieure de Cachan Cachan France Integrase of the human immunodeficiency virus type-1 HIV-1 recognizes specific sequences located in the U3 and U5 regions at the ends of viral DNA. We synthesized DNA duplexes mimicking the U5 region and containing either 2 -aminonucleosides or non-nucleoside 1 3-propanediol insertions at the third and terminal positions and studied their interactions with HIV-1 integrase. Both modifications introduced a local structural distortion in the DNA double helix. Replacement of the terminal nucleosides by corresponding 2 -aminonucleosides had no significant effect on integrase activity. We used an integrase substrate bearing terminal 2 -aminonucleosides in both strands to synthesize a duplex with cross-linked strands. This duplex was then used to determine whether terminal base pair disruption is an obligatory step of retroviral DNA 3 -processing. Processing of the cross-linked analog of the integrase substrate yielded a product of the same length as 3 -processing of the wild-type substrate but the reaction efficiency was lower. Replacement of the third adenosine in the processed strand by a corresponding 2 -aminonucleoside did not affect integrase activity whereas its replacement by 1 3-propanediol completely inhibited 3 -processing. Both modifications of the complementary thymidine in the nonprocessed strand increased the initial rate of 3 -processing. The same effect was observed when both
