HIV-1　integrase　(IN)　integrates　the　viral　DNA　into　the　host　cell　chromosome,　however,　the　binding　mode　of　IN　with　the　viral　DNA　and　the　integration　mechanism　remain　unclear.　In　this　paper,　molecular　docking　method　was　used　to　investigate　the　interactions　of　HIV-1　IN　dimer　with　the　8　bp　and　27　bp　segments　of　viral　DNA　before　the　3＇　processing　(3＇-P)　reaction,　and　the　specific　binding　mode　between　IN　and　its　substrate　27　bp　segments　of　viral　DNA　was　obtained.　The　results　show　that　IN　has　one　specific　DNA-binding　region　and　another　non-specific　DNA-binding　region.　The　key　residues　for　IN　dimer　binding　with　viral　DNA　are　K14,　R20,　K156,　K159,　K160,　K186,　K188,　R199　residues　in　chain　B　and　K219,　W243,　K244,　R262,　R263　residues　in　chain　A.　The　explanation　for　the　minimum　length　of　15　bp　viral　DNA　to　activate　IN　was　given　on　the　basis　of　the　docked　complex　structure.　Through　the　analysis　of　the　binding　energy,　it　was　found　that　non-polar　interactions　are　the　principal　factor　favoring　the　binding　between　IN　and　DNA;　whereas,　the　stable　association　of　viral　DNA　with　the　key　residues　are　mainly　driven　by　polar　interactions.　The　simulation　results　basically　agree　with　the　experimental　data,　which　provide　us　with　some　structural　information　for　the　drug　design　on　the　basis　of　the　structure　of　HIV-1　IN.