ABSTRACT
RNA secondary structures play an essential role in human immunodeficiency virus (HIV) and potentially in human papillomavirus (HPV). This chapter provides an overview of the known functional secondary structures in HIV-1 and proposes a possibly functional secondary structure in HPV-16. The transactivation response element (TAR) resides at the 5' end of the HIV genome, encompassing the first 60 nucleotides of the HIV-1 transcript. The binding of the Tat protein to the TAR RNA structure is required for transcription of the virus. An interesting aspect of the TAR sequence is that it also plays a role at the DNA level, where it binds cellular proteins as part of the transcriptional promoter. RRE-like elements are found in a wider variety of retroviruses than are TAR-like elements: throughout the lentiviruses, and in human T-cell leukemia virus type 1 and type 2. The secondary structure of TAR shows considerable variation among the human and simian immunodeficiency viruses.
