Fig. 2: Branaplam stabilizes -1A bulged 5′SS RNA binding to U1 snRNP.

A RNA oligos containing -1A bulged 5′SS. Shaded region indicates predicted base pairing interactions with the U1 snRNA (top). B Chemical structure of branaplam. C SPR showing the association and dissociation of 11bp-1A RNA across various concentrations of branaplam (0–5 µM) and at 10 nM U1 snRNP. D Dose response curve showing the fitted dissociation rates (k_off) of response units vs branaplam concentration for 11bp-1A (white circles) and 11bp (black circles) RNAs. Data for 11bp-1A is overlaid with the fitted equation to determine EC₅₀ value (1.3 ± 0.1 µM). E Fluorescence in arbitrary units (au) across time in seconds (s) of 1 nM 9bp-1A RNA binding to immobilized U1 in the presence of 100 nM U1-C plus (top) DMSO (0.33 Hz) or (bottom) 10 µM branaplam (0.11 Hz) overlaid with idealizations (black lines). F Dose response curves of 9bp-1A RNA binding to U1 snRNP vs branaplam concentration. The fraction bound at each branaplam concentration (white cirlcle) is overlaid with a fitted equation (solid red line) and the 95% confidence interval of the fitted equation (shaded red region) to estimate an EC₅₀ value (0.45 ± 0.17 µM). G Cumulative probability distribution of bound dwell times across branaplam concentrations (DMSO, N = 5216; 0.1 µM, N = 6234; 0.3 µM, N = 4811; 1 µM, N = 3640; 3 µM, N = 2211; 10 µM, N = 1503). H Cumulative probability distribution of bound dwell times at 1 nM 9bp-1A and 100 nM U1-C (grey circles, N = 3640) in presence of 1 µM branaplam overlaid with MLE of mono (blue dashed) and biexponential distributions (solid red). I Maximum likelihood estimates of (left) time constants (\({\tau }_{B}^{1}\) and \({\tau }_{B}^{2}\)) and (right) amplitude of \({\tau }_{B}^{2}\) of a biexponential distribution for bound dwell times at 1 nM 9bp-1A RNA and 100 nM U1-C across branaplam concentrations (mean ± SEM). Plotted parameters are computed across all single molecules for each branaplam concentration (DMSO, N = 5216; 0.1 µM, N = 6234; 0.3 µM, N = 4811; 1 µM, N = 3640; 3 µM, N = 2211; 10 µM, N = 1503). J Contour plots showing the correlation between successive bound event durations (\(i\) and \(i+1\)) within individual molecules. Dashed line is the identity line. Source data are provided as a Source data file.