Create your DNA box using DNA Polyominoes. The original publication describing the self-organised fabrication strategy can be found here: Self-assembly programming of DNA polyominoes - https://doi.org/10.1016/j.jbiotec.2016.08.017
DNApoly-v2.0 is an enhanced version of the DNApoly-v1.0 web server, designed to generate DNA cuboids with 4x3 or 4x4 face configurations. These cuboids are fabricated based on the schema of DNA polyominoes, an extension of the geometric principles of tetrominoes. The generator produces DNA sequences that conform to structural requirements, validated by secondary structure predictions using the ViennaRNA package (Lorenz et al., 2011).
DNApoly is a nature-inspired approach to construct biocomputers mimicking the 80s video game Tetris. You can construct three-dimensional structures by combining DNA walls (technical term, DNA network configurations). You can find the program to create these walls in this repository (DNApoly-v1.0). In this project, you can use the interactive python notebook N_construct to generate links to combine these walls into a box. You can change the box dimensions by modifying the number of walls.
- Python 3.x
- Jupyter Notebook
- You need to run DNAPoly v1.0 to generate the relevant DNA network configuratios (3x4, or 4x4).
DNApoly-v1.0is available in this repository for local installation. You need to runRNAStructure(https://www.urmc.rochester.edu/rna/) to run the sequence-structure optimisation mode. You need to install the package locally on your machine.
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Please cite this article if you are running
DNApoly-v1.0:
DNA Tetrominoes: The Construction of DNA Nanostructures Using Self-Organised Heterogeneous Deoxyribonucleic Acids Shapes Ong HS, Rahim MS, Firdaus-Raih M, Ramlan EI (2015) DNA Tetrominoes: The Construction of DNA Nanostructures Using Self-Organised Heterogeneous Deoxyribonucleic Acids Shapes. PLOS ONE 10(8): e0134520. https://doi.org/10.1371/journal.pone.0134520 -
Please cite this articule if you are running
RNAStructure:
Reuter, J.S., Mathews, D.H. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11, 129 (2010). https://doi.org/10.1186/1471-2105-11-129
- Clone this repository: git clone https://github.com/eiramlan/DNApoly.git
- Start Jupyter Notebook: jupyter notebook
- Open the notebook file:
N_contruct.ipynb - Follow the instructions in the notebook to run the program.
This research is supported by the Prototype Development Research Grant Scheme (PRGS) PR001-2018A from the Ministry of Higher Education, Malaysia.
This project is licensed under the GNU General Public License v3.0. See the LICENSE file for more details.