Structural basis for the specificity of the initiation of HIV-1 reverse transcription

Initiation of human immunodeficiency virus type I (HIV-1) reverse transcrip tion requires specific recognition of the viral genome, tRNA(3)(Lys), which acts as primer, and reverse transcriptase (RT), The specificity of this te rnary complex is mediated by intricate interactions between HIV-1 RNA and t RNA(3)(Lys), hot remains poorly understood at the three-dimensional level, We used chemical probing to gain insight into the three-dimensional structu re of the viral RNA-tRNA(3)(Lys) complex, and enzymatic footprinting to del ineate regions interacting with RT, These and previous experimental data we re used to derive a three-dimensional model of the initiation complex. The viral RNA and tRNA(3)(Lys) form a compact structure in which the two RNAs f old into distinct structural domains. The extended interactions between the se molecules are not directly recognized by RT, Rather, they favor RT bindi ng by preventing steric clashes between the nucleic acids and the polymeras e and inducing a viral RNA-tRNA(3)(Lys) conformation which fits perfectly i nto the nucleic acid binding cleft of RT, Recognition of the 3' end of tRNA (3)(Lys) and of the first template nucleotides by RT is favored by a kink i n the template strand promoted by the short junctions present in the previo usly established secondary structure.