DOI: 10.5281/zenodo.17187773
title: Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures

description: Title: Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures

 

Authors (w/ORCID):

Rupam Saha* - 0009-0000-9567-3010

Daichi Hayakawa* - 0000-0002-2783-5943

Thomas E Videbæk - 0000-0001-9158-2824

Mason Price - 0009-0009-6706-9671

Wei-Shao Wei - 0000-0001-9467-4273

Juanita Pombo -

Daniel Duke - 0009-0004-9952-445X

Gaurav Arya - 0000-0002-5615-0521

Gregory M Grason -  0000-0001-5479-9370

W Benjamin Rogers - 0000-0001-8587-8215

Seth Fraden - 0000-0002-2420-9939

 

Funding:

This work is supported by the Brandeis University Materials Research Science and Engineering Center, which is funded by the National Science Foundation under award number DMR-2011846. G.A. acknowledges support from the National Science Foundation (Grant no. CMMI-2323969). TEM images are prepared and imaged at the Brandeis Electron Microscopy facility. Computational resources were provided by the Duke Computing Cluster and the ACCESS program supported by the National Science Foundation (Grants nos. ACI-2138259, 2138286, 2138307, 2137603, and 2138296).

 

Description:

This repository contains images and data for the publication “Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures” (https://arxiv.org/abs/2502.05388). In this article, we analyze the binding angle of DNA origami building blocks using double-stranded DNA overhangs and self-assemble deltahedral shells, T=13 icosahedral shell and toroid. 

 

************* Cryo-EM ************

Here, we have provided the binding angle distributions in .xlsx files for 3 cryo-EM designs 6-delta, 10-delta and negative 7-delta, obtained at 136K temperature. This data is plotted in Fig. 2C and S9. 

Additionally, The post-processed maps of cryo-EM data are deposited in the Electron Microscopy Data Bank with accession codes:





EMD-48566 [https://www.ebi.ac.uk/emdb/EMD-48566], 




EMD-48565 [https://www.ebi.ac.uk/emdb/EMD-48565], 




EMD-48567 [https://www.ebi.ac.uk/emdb/EMD-48567], 




EMD-48569 [https://www.ebi.ac.uk/emdb/EMD-48569].



 

************* OxDNA ************

We have provided oxDNA simulation results of Dimer configuration (side1-side2 binding) at 298K temperature, including the PDB files for both positive and negative binding angles, screened from 0-delta to 20-delta. 

Additionally, there are two .csv files containing the binding angles as a function of frames and n-delta. These data have been used at Fig. 2D and 2L.

 

************* Gel electrophoresis ************

We have provided laser-scanned images of gel electrophoresis in uncropped and unedited versions. For the ease of the future readers, we have provided an excel file (figures.xlsx) that contains the file names (uncropped gel) and the corresponding figures where the data has been used. 

 

************* T13 ************

We have provided the TEM images of the T13 assembly. We have analyzed these TEM images to calculate the distribution of hexagonal edge lengths and surface area of T13 shells. 

The hexagonal edge lengths measurements can be found at T13_hexagonal_edge_length_measurements(micron).xlsx, presented at Fig 4C and S25D.

The surface area measurements can be found at 

T13_surface_area_measurements(nm_sq).xlsx, presented at Fig. S25D. 

 

************* Toroid ************

We have provided the Transmission electron microscopy (TEM) images of the toroid assembly. We have interpreted these images to calculate the selectivity of the fully closed 4-fold and 5-fold toroids (Fig. S28C), available at closedToroidsRatio.xlsx.

Additionally, we have provided the distribution of the bend angles of the open toroids interpreted from the TEM images (Fig. S28G), available at opened_tubule_angle_distribution.xlsx.