A　QM-MM　calculation　was　carried　out　to　study　the　mechanism　of　DNA　cleavage　by　the　dipeptide　seryl-histidine　(SH).　The　effective　molecular　recognition　between　SH　and　DNA　through　multi-hydrogen-bonds　was　obtained,　as　well　as　the　corresponding　structural　parameters.　The　results　could　be　used　to　explain　the　mechanism　of　DNA　cleavage　by　SH,　which　supposed　that　the　formation　of　penta-coordinate　phosphorus　intermediate　caused　the　phosphodiester　bond　hydrolysis.