Fig. 5: Topology of nanosprings revealed by coarse-grained simulation.

a Trajectory of root mean square deviation (RMSD) as an index for simulation equilibration. To compute the RMSD, the squared distance from the initial position at 0 ns was computed for each entity at each time step, and root mean of the values were plotted. Horizontal and vertical axes are time and RMSD, respectively. Red solid and black dotted lines correspond to the 21 bp and 4 nt linker structures. b Visualization of root mean square fluctuation (RMSF) of the last 1 µs as an index of thermal fluctuation (21 bp linker on the left; 4 nt linker on the right). To compute the RMSF, the squared distances from reference position were computed for a total of 100 frames of simulation from 2000 to 3000 ns for each entity. The reference position for each entity was defined as the averaged coordinate of the 100 frames. Each entity of oxDNA at the last frame of simulation is colored by the RMSF values ranging from 2 to 10 nm (outlier values smaller or larger than 2 or 10 nm thresholds have the same colors of 2 or 10 nm, respectively). c Snapshot of the structures at 3 µs of the simulation. The entities of backbone and pier used for the computation are emphasized in green and magenta spheres. d Differences of radius of fitted helix between backbone and pier, and between the 21 bp and 4 nt linker structures (n = 100 for each measurement). In the graph, red dots are outlier points which are excluded from analysis, boxes represent the first and third quartiles, middle line shows the median, cross point is the mean, and the whiskers show minimum and maximum values. Source data are provided as a Source Data file.