The invention relates to pseudorotaxane molecular compound produced by cucurbit[6]uril and 1, 6-di-imidazole group di-acid salt whose chemical molecular formula is C36H36N24O12*C12H20N4*2X*nH2O whose X equals to Cl, H2PO4, HSO4, NO3, Br; n is not less than 1. The compound can be used in nucleic acid cutting whose condition is that the cutting reagent is dissolved in buffer system solution with given pH value, then mixed with cutting substrate; their final density is kept in given range; and their temperature is also kept in given range. The cutting reagent can be used to cut nucleic acid in short time at physiology condition, further study the application in gene therapy medicine preparation to develop into gene therapy medicine.