Probing Retroviral and Retrotransposon Genome Structures: The “SHAPE” of Things to Come

Figure 2

Examining RNA/DNA structural dynamics by combining chemical acylation with mass spectrometry. Left, Nano-ESI mass spectra of a model HIV-1 PPT RNA/DNA hybrid following treatment with a 10-fold (a), 50-fold (b), and 100-fold NMIA excess (c). At limiting NMIA concentrations (a) and (b), the majority of the PPT RNA is unmodified, and RNAs containing one, two, three, or four NMIA adducts can be observed, while excess acylation (c) results in overmodification of the entire RNA strand. In all cases, however, the PPT DNA complement is not modified by NMIA owing to the absence of a ribose 2′-OH group. Right, NMIA sensitivity of the wild type (a) and dF-modified (b) and (c) HIV-1 PPT RNA/DNA hybrids. In all cases, DNA and RNA nucleotides are represented in green and blue, respectively. NMIA-sensitive ribonucleotides are in yellow and positions of dF substitution in red. The position of the PPT/U3 junction has been indicated. Adapted from [29].