The molecular recognition of macrocyclic polyamines (MP-1,MP-2 and MP-3) to RNA, and its effects on apoptosis of cos-7 cells were studied in order to explore their mechanism of anti-HIV-1 activity. Cleavage of RNA was observed by agarose electrophoresis; and apoptosis was determined by flow cytometry assay. Computer modeling was used to investigate the theoretical possibility of compounds binding to TAR RNA. Results showed that: (1) Compounds MP-1,MP-2 and MP-3 could not only cleave the polyA·polyU and TAR RNA, but also inhibit the interaction of Tat-RNA. (2) Compounds could affect the percentage of hypodiploid cell. It is proposed that compounds MP-1,MP-2 and MP-3 could recognize the polyA·polyU and TAR RNA molecules and cleave them, and affect the interaction of Tat-RNA. The compounds may affect the apoptosis of cos-7 cells.