DOI: 10.5281/zenodo.17109136
title: From toroids to helical tubules: Kirgami-inspired programmable assembly of two-periodic curved crystals from DNA origami

description: This repository contains images and measurement data for the publication “From toroids to helical tubules: Kirigami-inspired programmable assembly of two-periodic curved crystals” (https://arxiv.org/abs/2506.16403). In this article, we use DNA origami to program the self-assembly of toroids, left- and right-handed helical tubules, and serpentine tubules. 

We provide experimental transmission electron micrographs that were used for the probability distributions reported in Figure 4 E-H of the main text. There are four CSV files with the measurements and the corresponding file name from which the measurements were taken. The folders are associated with the CSV files as follows. 





EM-images-toroid | “Toroid-Measurements.csv”




EM-images-left-handed-helix | “LH-Helix-Measurements.csv”




EM-images-right-handed-helix | “RH-Helix-Measurements.csv”




EM-images-serpentine | “Serpentine-Measurements.csv”



There are two MATLAB scripts that can be used to reproduce the histograms in Figure 4 of the main text. The script “hist_toroid_R.m” is used for the toroid plot in Fig. 4E(d). The script “hist_pitch.m” is used for the helical and serpentine histograms in Fig. 4F-H(d). 

We include the tomography data reported in Fig. 4F-H(e) of the main text. In the tomogram folders for the left- and right-handed helical tubules, we include the corresponding ".st" file (which can be opened using the open-source tool IMOD) and a video composed of every slice from the tomographic reconstruction. For each folder, we also include unedited representative snapshots of slices at different heights.

We include data for the simulation results used in Figure 5 of the main text and Figure S12 in the Supplementary Information. The simulation results are stored in the folders “Simulation-results-toroid” and “Simulation-results-helix” for the main text figure and "Simulation-results-SI-helix-5121" for the SI figure. The vertex coordinate data for all simulations are stored in the file “coordinates.zip”. Each simulation is stored as a CSV file, whose title specifies the conditions of the simulation. The face data is stored in the file “faces.zip”, where each row represents a face. The first three entries in a row specify the vertex indices from the corresponding coordinates file, and the fourth entry is the species of that triangle. The frequencies of each assembly outcome are stored in the file “outcome_frequencies.zip”. 

Lastly, we include the simulation data used in Section 4B of the SI. In “Simulation-results-overlap-analysis.zip”, we include four zip files separated based on the most prevalent assembly outcome: on-target, off-target, overgrown, and undernucleated. Then, within each zip file, there are folders for varying excluder sizes that contain the corresponding simulation data. The name of the folder specifies the conditions of the simulations and excluder radius. The vertex coordinate data are stored in folders that end in “coordinates”, while the face data are stored in folders that end in “faces”, both of which are in the same format as above. In “Simulation-results-intersection-counts.zip” we include all of the coordinate and face data used for Figure S11, which come from the same simulations as in Fig. S10A, but with a higher number of snapshots over time. We store our time-intersection analysis of this data in JSON files in the folder “Intersection counts”, which can be used to reproduce the plots in Fig. S11 using the Python script “plotIntersectionCountsOverTime.py”.