Nonradioactive Methods for the Detection of RNA-Protein Interaction

Abstract

RNA in biological systems is associated with proteins. Recent work in eukaryotes has identified common motifs present in families of RNA-binding proteins. Usually, RNA-binding proteins recognize both sequence and structure at their target sites. Therefore, identification of proteins that interact with a specific RNA sequence contributes to the understanding of biological processes. Thus, the genome of human immunodeficiency virus (HIV) encodes proteins, Tat, Rev and NC, that bind to specific viral RNA motives (1,2). These interactions mediate different steps of virus replication i.e., transactivation of transcription, nuclear export of viral transcripts, or packaging of two RNA genomes into the mature virion. In addition, we recently reported that Nef, an accessory protein encoded by HIV-1, belongs to the family of RNA-binding proteins (3). Using different-size variant proteins and point-mutated proteins, it was found that the amino terminal Arg-rich domain of Nef is involved in the RNA-binding activity. Nef proteins from HIV-2 and SIV (simian immunodeficiency virus) also showed RNA-binding capacity (4).