Extended Data Fig. 2: DREEM clustering identifies and quantifies individual structures from in vitro mixing experiments. | Nature

Extended Data Fig. 2: DREEM clustering identifies and quantifies individual structures from in vitro mixing experiments.

From: Determination of RNA structural diversity and its role in HIV-1 RNA splicing

Extended Data Fig. 2

Structure 1 and structure 2 sequences were in vitro-transcribed and refolded, mixed in different proportions and probed with DMS-MaPseq. The region used for DREEM clustering covers nucleotides 21–135 (labelled as 1–115 on the figure), which excludes the primers used for RT–PCR (that have no DMS-induced mutations) and is identical in sequence for the two structures, except for the A > C mutation at position 94. Position 94 is masked during analysis. The topmost panel shows the DMS reactivity pattern of structure 1 by itself and structure 2 by itself. The rest of the panels show the clustering results at specified mixing ratios (n = 1).

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