HIV-1　integrase　(IN)　is　an　essential　enzyme　for　viral　replication　cycle　and　a　widely　held　assumption　is　that　functional　IN　acts　as　a　tetramer.　The　association　of　the　IN　tetramer　with　eight　different　length　segments　of　viral　end　DNA　were　investigated　by　using　DOT　package.　Based　on　the　eight　bindings,　the　DNA　binding　regions　of　IN　tetramer　and　the　influence　of　the　length　of　viral　DNA　to　the　association　were　explored.　The　results　indicate　that　there　are　three　DNA　binding　regions　of　IN　tetramer　for　viral　DNA.　Further,　two　regions　are　the　viral　DNA　binding　regions,　and　the　rest　are　the　host　DNA　binding　region.　All　of　the　above　simulation　results　agree　well　with　experimental　data,　which　provide　us　a　more　complete　structural　basis　for　guiding　drug　discovery　and　reveling　integration　mechanism.