Fig. 1.

Distribution of functional domains in viral genomic RNA. The 5′UTR consists of many highly structured elements such as the TAR/polyA domain of HIV-1 (Jones et al., 2014), HIV-1 tRNA-like PBS/TLE domain (Jones et al., 2014) and the HCV IRES (Perard et al., 2013), all modeled based on SAXS data. NMR spectroscopy has yielded high-resolution structures of small sections of the HIV-1 frameshift signal (Staple and Butcher, 2005) and RRE export signal (Battiste et al., 1996), both located within coding regions. A SAXS-derived model of the full-length HIV-1 RRE has also recently been published (Fang et al., 2013). Large, structured RNAs within the 3′UTR of plant viral genomes have also been shown to be functional; for example, the BMV TLS (Felden et al., 1994) and TCV 3′CITE (Zuo et al., 2010) were modeled using probing data and a combination SAXS/NMR approach, respectively.