Secondary structure of the HIV‑1 genome

Abstract

Evaluation of: Watts JM, Dang KK, Gorelick RJ: Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460(6), 711–716 (2009). The ssRNA, comprising the HIV genome, present as a doublet in HIV-1, has the ability of all RNA molecules to fold using Watson–Crick and noncanonical base pairing to form helices and loops, which are themselves functional as protein- and RNA-binding sites that regulate many stages of the viral lifecycle. This article explores the ability of a single technique (SHAPE) to map these structures in full length HIV RNA and attempts to suggest functions associated with these structures. The demonstration of a novel rapid technique that can generate extensive base by base data is an important achievement and it is useful to see this technique being publicized. This well-presented article is an attractive showpiece for the capabilities of SHAPE. However, some of the data are ambiguous and some are subject to alternative interpretations. SHAPE is a useful additional rapid...