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. 2023 Jan 24;14:382. doi: 10.1038/s41467-023-36156-1

Fig. 4. Per-nucleotide stabilities of RNA-scaffolded origami revealed by DMS-MaPseq.

Fig. 4

a Dual-duplex antiparallel crossover (DX) edge comprising RNA scaffold (light grey) and DNA staple (dark grey) strands. One example of each structural feature is labeled on the involved scaffold base (because DMS-MaPseq probes only RNA). DX1: single crossover, DX2: double crossover, term: terminus, 5’ and 3’: ends (with respect to scaffold) of unbroken segments of RNA:DNA duplex. b Distributions of DMS reactivities among adenines and cytosines within 6 bp of each type of feature in n = 5 independent A-form origami (rT55, rT66, rT77, rO66, rPB66). Positions −1 and 1, respectively, lie immediately 5’ and 3’ of the feature and correspond to segment 3’ and 5’ ends labeled in (a). Each box plot depicts the median (middle line), 1st and 3rd quartiles (box), minimum/maximum up to 1.5 interquartile ranges from box (whiskers), and outliers (grey diamonds). P-values indicate significance of median reactivities exceeding those among all positions further from the feature on the same side (one-sided Mann-Whitney U test). c Comparison of predicted melting temperatures and mean DMS reactivities among interior (excluding 5’ and 3’ ends) adenines and cytosines of n = 490 segments. Each point depicts one segment whose 5’ and 3’ end features determine the point’s shape and color, respectively. d Destabilization of base pairs at segment ends. For each segment, the ratio between the DMS reactivity of its 5’ (3’) terminal nucleotide (if adenine or cytosine) and the mean DMS reactivity among its interior adenines and cytosines is plotted on the left (right), above the feature at the 5’ (3’) end of the segment. Black bars show means. Upper P-values indicate significance of the median ratios exceeding unity (one-tailed Wilcoxon signed-rank test); P-values connecting pairs of features indicate significance of differences between the median ratios of the features (two-tailed Mann–Whitney U test). e Similar to (d), but separately analyzing DMS reactivities of adenines (A-T pairs) and cytosines (C-G pairs). Arrows point from mean ratios among C-G pairs to A-T pairs. P-values indicate significance of differences between the median ratios of A-T and C-G pairs (two-tailed Mann–Whitney U test). Source data are provided as a Source Data file.