SNUPI

SNUPI is a multiscale analysis framework for the prediction of structured DNA assemblies.

Updates

• v3.10 (2024-07-29)
  • EtBr-binding simulations
• v3.01 (2024-01-24)
  • Minor error fix
• v3.00 (2023-09-27)
  • Dynamic simulations
  • Restarting simulations
  • GPU acceleration
• v2.01 (2022-01-18)
  • Minor error fix
• v2.00 (2021-11-19)
  • Analysis of wireframe or topologically-closed designs
  • export of the oxDNA input file format.
  • Improved modeling of the single-stranded DNA
• v1.01 (2021-02-23)
  • Support for command line execution (see protocol.pdf)
  • Support for mac and linux
  • Minor error fix
• v1.00 (2021-01-07)
  • Initial upload

Prerequisite

• The correct version of the MATLAB Runtime should be installed.
• v3: Runtime version R2022b (9.13)
• v2: Runtime version R2019a (9.6)
• v1: Runtime version R2019a (9.6)
• Download link: http://www.mathworks.com/products/compiler/mcr/index.html

How to run (Window)

• Execute 'SNUPI.exe'
• The example result files will be saved in the 'OUTPUT' folder.
• To analyze custom design files, modify 'Input.txt'

How to run (Linux)

• Open the terminal
• Move the current directory to the SNUPI folder
• Give permission to execute
  • chmod +x *
• Execute SNUPI
  • ./run_SNUPI.sh <mcr_directory>
• For example,
  • ./run_SNUPI.sh /usr/local/MATLAB/MATLAB_Runtime/R2022b
• The result files will be saved in the 'OUTPUT' folder.
• To analyze custom design files, modify 'Input.txt'

How to run (Mac)

• Open the terminal
• Move the current directory to the SNUPI folder
• Give permission to execute
  • chmod +x *
• Execute SNUPI in the FILE folder using Terminal
  • ./run_SNUPI.sh <mcr_directory>
• For example,
  • ./run_SNUPI.sh /Applications/MATLAB/MATLAB_Runtime/R2022b
• The result files will be saved in the 'OUTPUT' folder.
• To analyze custom design files, modify 'Input.txt'

Assign design files

• Modify the 'Input.txt' file to assign design files.
• In the 'Input.txt' file, <lattice_type> and <file_directory> should be denoted.
• Use caDNAno design files (json and csv).
• The percentage mark ('%') represents comments
• Example designs were already assigned.

Technical details

• SNUPI framework (static analysis): Rapid computational analysis of DNA origami assemblies at near-atomic resolution, ACS Nano (2021), https://doi.org/10.1021/acsnano.0c07717
• Improved model of single-stranded DNA: Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies, ACS Nano (2021), https://doi.org/10.1021/acsnano.1c08861
• Partition and relocation framework (free-form structures): Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint, ACS Nano (2022), https://doi.org/10.1021/acsnano.1c10347
• Langevin dynamics simulations: A computational model for structural dynamics and reconfiguration of DNA assemblies, Nature Communications (2023), https://doi.org/10.1038/s41467-023-42873-4
• Graph neural network (Deep SNUPI): Prediction of DNA origami shape using graph neural network, Nature Materials (2024), https://doi.org/10.1038/s41563-024-01846-8
• EtBr-binding simulations: Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies, Nature Communications (2023), https://doi.org/10.1038/s41467-024-50871-3