CHARACTERIZATION OF A KISSING HAIRPIN COMPLEX DERIVED FROM THE HUMAN-IMMUNODEFICIENCY-VIRUS GENOME

Base-pair formation between two hairpin loops-a ''kissing'' complex-is an RNA-folding moth that links two elements of RNA secondary structur e. It is also a unique protein recognition site involved in regulation of ColE1 plasmid DNA replication. The trans-activation response eleme nt (TAR), a hairpin and bulge at the 5' end of the untranslated leader region of the human immunodeficiency virus 1 mRNA, enhances the trans cription Of the virus and is necessary for viral replication. Gel elec trophoresis and absorbance melting curves indicate that a synthesized RNA hairpin (Tar-16) with a loop sequence complementary to the TAR lo op sequence (CUGGGA) associates specifically with a 16-nucleotide TAR hairpin (Tar-16) to form a stable complex. RNase T1 probing indicates that the three guanines in the Tar-16 loop become inaccessible in the complex. NMR imino proton spectra reveal that 5 base pairs are formed between the two hairpin loops (Tar-16 and Tar-16); only the adenine a t the 3' terminus of the TAR loop does not form a base pair with the 5 '-terminal uracil of the complementary loop. A 14-nucleotide hairpin [ CCUA-(UCCCAG)UAGG] with a loop sequence complementary to the TAR loop is conserved within the gag gene of human immunodeficiency virus 1. A synthesized RNA hairpin corresponding to this conserved sequence also binds to the Tar-16 hairpin with high affinity. It is possible that th e same RNA loop-loop interaction occurs during the viral life cycle.