HIV-1　integrase　(IN)-catalyzed　strand　transfer　is　a　divalent　cationic　cofactor　dependent　reaction　which　involves　IN-DNA　interaction.　In　this　work,　viral　DNA　substrates　with　different　lengths　were　used.　The　strand　transfer　activity　of　IN　with　these　DNA　substrates　in　the　presence　of　Mn2+　and　Mg2+　were　investigated,　as　well　as　some　other　reaction　characters　related　with　IN-DNA　interaction.　It　is　found　that　the　strand　transfer　activity　is　both　divalent　cation　and　viral　DNA　length　dependent.　The　reaction　conditions　for　the　wild　type　IN　are　stricter　than　those　of　soluble　mutant　IN.　Moreover,　IN　significantly　prefers　E　strand　over　A　strand　as　the　target　strand,　and　both　the　recessed　and　blunt　end　viral　DNA　have　similar　strand　transfer　activity　in　the　presence　of　either　metal　ion.　This　work　provides　valuable　insight　for　the　understanding　of　IN-DNA　interaction　and　will　be　helpful　in　the　anti-IN　drug　development.　©2009　IEEE.