Extended Data Fig. 1: MD simulation of the structure of the ARPLA system.

(a) A representation of the ARPLA system with different sites (site 1-6) chosen to analyze distances; (b) A representative structure from the simulation with oxDNA, including the glycan probe, the RNA binding probe, the connector 1, and the connector 2. The circle of the connector 1 and the connector 2 tends to form a triangle structure, with two sides formed by DNA helix and one side formed by the ssDNA region in the connector 1; (c) The distributions of the distance between interested sites. 3 sets of distances were calculated with oxDNA tool¹², including the distances between the edges of the connector 1 ssDNA region (site 1 and site 2), between the ends of spacers of the Glycan probe and the RNA binding probe (site 3 and site 4), and between the predicted glycan binding site³⁶ and the center of the RISH site (site 5 and site 6). The distance between site 1 and site 2 is in the range of 1-14 nm, with an average around 7 nm. The results agree with the B-form DNA length of the connector 1 ssDNA region (43 nt, around 14.3 nm), with the consideration of ssDNA bending and folding. The distance between site 3 and site 4 is in the range of 5-15 nm, with an average around 10 nm. The distance between site 5 and site 6 is in the range of 5-20 nm, with an average around 15 nm.