Isolation and characterization of an RNA that binds with high affinity to Tat protein of HIV-1 from a completely random pool of RNA

The trans-activation (Tat) protein of human immunodeficiency virus type-1 (HIV-1) is vital for the replication of the virus. In a transcription assay i n v i t r o in the presence of authent ic TAR RNA, we found that authentic TAR RNA inhibits transcription from a template based on the CMV early promoter in a manner that is not related to the Tat/TAR interaction. Using variants of TAR RNA, we identified potential sequences of RNA that seems to be responsible for the inhibition of transcription. In addit ion, we isolated an RNA aptamer that can bind with high aff inity to Tat protein specifically. The isolated aptamer appears to include two TAR-like RNA motifs for higheraff inity binding to Tat peptides. The aptamer's high affinity for Tat peptides, as wel l as the absence of any inhibitory effects on the transcription of unrelated genes, as opposed to those of TAR RNA, suggests that the novel RNA might be very useful as a Tat-specific decoy.