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Resolving alternate conformers of the HIV-1 5′UTR by in-gel SHAPE. (A) Schematic depicting native polyacrylamide gel electrophoresis of in vitro-transcribed HIV-1 5′ UTR RNA to resolve the monomer (M) and dimer species (D), which are excised and treated with the SHAPE reagent in situ. (B) Following recovery of chemically modified RNAs, the SHAPE protocol is completed, revealing the monomeric and dimeric configurations of the 5'UTR construct. Adapted from Kenyon et al. (2013).
