Recent　studies　direct　the　researchers　into　building　DNA　computing　machines　with　intelligence,　which　is　measured　by　three　main　points:　autonomous,　programmable　and　able　to　learn　and　adapt.　Logical　inference　plays　an　important　role　in　programmable　information　processing　or　computing.　Here　we　present　a　new　method　to　perform　autonomous　molecular　forward　inference　for　expert　system.　A　novel　repetitive　recognition　site　(RRS)　technique　is　invented　to　design　rule-molecules　in　knowledge　base.　The　inference　engine　runs　autonomously　by　digesting　the　rule-molecule,　using　a　Class　LIB　restriction　enzyme　Ppil.　Concentration　model　has　been　built　to　show　the-feasibility　of　the　inference　process　under　ideal　chemical　reaction　conditions.　Moreover,　we　extend　to　implement　a　triggering　communication　between　molecular　automata,　as　a　further　application　of　the　RRS　technique　in　our　model.