The caDNAno Repository

This is a repository of caDNAno designs that have been recreated for usage alongside my research at the Shenzhen Lansi Institute of A.I. in Medicine. Each design is saved in the original caDNAno v2 JSON format and can only be opened with caDNAno or a similar program.

Please feel free to let me know of any errors or designs you'd like recreated. I'm happy to continually expand upon this repository!

List of caDNAno Designs from Published Research Articles

The following is a list of caDNAno designs that can currently be found in this repository, sorted by PubMed ID number and listed with the name of the research article the design was originally found in and its associated APA citation.

• PMID 22092186 - Cellular immunostimulation by CpG-sequence-coated DNA origami structures

  • Schüller, V. J., Heidegger, S., Sandholzer, N., Nickels, P. C., Suhartha, N. A., Endres, S., Bourquin, C., & Liedl, T. (2011). Cellular immunostimulation by CpG-sequence-coated DNA origami structures. ACS Nano, 5(12), 9696–9702. https://doi.org/10.1021/nn203161y

• PMID 22950811 - DNA origami delivery system for cancer therapy with tunable release properties

  • Zhao, Y.-X., Shaw, A., Zeng, X., Benson, E., Nyström, A. M., & Högberg, B. (2012). DNA origami delivery system for cancer therapy with tunable release properties. ACS Nano, 6(10), 8684–8691. https://doi.org/10.1021/nn3022662

• PMID 24351090 - DNA origami-compliant nanostructures with tunable mechanical properties

  • Zhou, L., Marras, A. E., Su, H.-J., & Castro, C. E. (2014). DNA Origami Compliant Nanostructures with Tunable Mechanical Properties. ACS Nano, 8(1), 27–34. https://doi.org/10.1021/nn405408g

• PMID 24532395 - DNA origami structures directly assembled from intact bacteriophages

  • Nickels, P. C., Ke, Y., Jungmann, R., Smith, D. M., Leichsenring, M., Shih, W. M., Liedl, T., & Högberg, B. (2014). DNA origami structures directly assembled from intact bacteriophages. Small (Weinheim an Der Bergstrasse, Germany), 10(9), 1765–1769. https://doi.org/10.1002/smll.201303442

• PMID 24963790 - DNA origami as an in vivo drug delivery vehicle for cancer therapy

  • Zhang, Q., Jiang, Q., Li, N., Dai, L., Liu, Q., Song, L., Wang, J., Li, Y., Tian, J., Ding, B., & Du, Y. (2014). DNA origami as an in vivo drug delivery vehicle for cancer therapy. ACS Nano, 8(7), 6633–6643. https://doi.org/10.1021/nn502058j

• PMID 25136758 - Addressing the instability of DNA nanostructures in tissue culture

  • Hahn, J., Wickham, S. F. J., Shih, W. M., & Perrault, S. D. (2014). Addressing the instability of DNA nanostructures in tissue culture. ACS Nano, 8(9), 8765–8775. https://doi.org/10.1021/nn503513p

• PMID 26248642 - A self-assembled DNA origami-gold nanorod complex for cancer theranostics

  • Jiang, Q., Shi, Y., Zhang, Q., Li, N., Zhan, P., Song, L., Dai, L., Tian, J., Du, Y., Cheng, Z., & Ding, B. (2015). A Self-Assembled DNA Origami-Gold Nanorod Complex for Cancer Theranostics. Small (Weinheim an Der Bergstrasse, Germany), 11(38), 5134–5141. https://doi.org/10.1002/smll.201501266

• PMID 26583570 - Daunorubicin-loaded DNA origami nanostructures circumvent drug-resistance mechanisms in a leukemia model

  • Halley, P. D., Lucas, C. R., McWilliams, E. M., Webber, M. J., Patton, R. A., Kural, C., Lucas, D. M., Byrd, J. C., & Castro, C. E. (2016). Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model. Small (Weinheim an Der Bergstrasse, Germany), 12(3), 308–320. https://doi.org/10.1002/smll.201502118

• PMID 27053991 - Design and construction of a DNA origami drug delivery system based on MPT64 antibody aptamer for tuberculosis treatment

  • Ranjbar, R., & Hafezi-Moghadam, M. S. (2016). Design and construction of a DNA origami drug delivery system based on MPT64 antibody aptamer for tuberculosis treatment. Electronic Physician, 8(2), 1857–1864. https://doi.org/10.19082/1857

• PMID 28423273 - Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations

  • Shi, Z., Castro, C. E., & Arya, G. (2017). Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS Nano, 11(5), 4617–4630. https://doi.org/10.1021/acsnano.7b00242

• PMID 29431737 - A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo

  • Li, S., Jiang, Q., Liu, S., Zhang, Y., Tian, Y., Song, C., Wang, J., Zou, Y., Anderson, G. J., Han, J.-Y., Chang, Y., Liu, Y., Zhang, C., Chen, L., Zhou, G., Nie, G., Yan, H., Ding, B., & Zhao, Y. (2018). A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nature Biotechnology, 36(3), 258–264. https://doi.org/10.1038/nbt.4071

• PMID 30216608 - Pharmacophore nanoarrays on DNA origami substrates as a single-molecule assay for fragment-based drug discovery

  • Kielar, C., Reddavide, F. V., Tubbenhauer, S., Cui, M., Xu, X., Grundmeier, G., Zhang, Y., & Keller, A. (2018). Pharmacophore Nanoarrays on DNA Origami Substrates as a Single-Molecule Assay for Fragment-Based Drug Discovery. Angewandte Chemie (International Ed. in English), 57(45), 14873–14877. https://doi.org/10.1002/anie.201806778

• PMID 30288887 - A tailored DNA nanoplatform for synergistic RNAi-/chemotherapy of multidrug-resistant tumors

  • Liu, J., Song, L., Liu, S., Zhao, S., Jiang, Q., & Ding, B. (2018). A Tailored DNA Nanoplatform for Synergistic RNAi-/Chemotherapy of Multidrug-Resistant Tumors. Angewandte Chemie (International Ed. in English), 57(47), 15486–15490. https://doi.org/10.1002/anie.201809452

• PMID 31883145 - DNA origami post-processing by CRISPR-Cas12a

  • Xiong, Q., Xie, C., Zhang, Z., Liu, L., Powell, J. T., Shen, Q., & Lin, C. (2020). DNA Origami Post-Processing by CRISPR-Cas12a. Angewandte Chemie (International Ed. in English), 59(10), 3956–3960. https://doi.org/10.1002/anie.201915555

• PMID 32573062 - An intelligent DNA nanorobot for autonomous anticoagulation

  • Yang, L., Zhao, Y., Xu, X., Xu, K., Zhang, M., Huang, K., Kang, H., Lin, H.-C., Yang, Y., & Han, D. (2020). An Intelligent DNA Nanorobot for Autonomous Anticoagulation. Angewandte Chemie (International Ed. in English), 59(40), 17697–17704. https://doi.org/10.1002/anie.202007962

• PMID 32623634 - Design and simulation of a DNA origami nanopore for large cargoes

  • Khosravi, R., Ghasemi, R. H., & Soheilifard, R. (2020). Design and Simulation of a DNA Origami Nanopore for Large Cargoes. Molecular Biotechnology, 62(9), 423–432. https://doi.org/10.1007/s12033-020-00261-z

• PMID 32873796 - Rational design of DNA nanostructures for single molecule biosensing

  • Raveendran, M., Lee, A. J., Sharma, R., Wälti, C., & Actis, P. (2020). Rational design of DNA nanostructures for single molecule biosensing. Nature Communications, 11(1), Article 1. https://doi.org/10.1038/s41467-020-18132-1

• PMID 33089613 - A tubular DNA nanodevice as a siRNA/chemo-drug co-delivery vehicle for combined cancer therapy

  • Wang, Z., Song, L., Liu, Q., Tian, R., Shang, Y., Liu, F., Liu, S., Zhao, S., Han, Z., Sun, J., Jiang, Q., & Ding, B. (2021). A Tubular DNA Nanodevice as a siRNA/Chemo-Drug Co-delivery Vehicle for Combined Cancer Therapy. Angewandte Chemie (International Ed. in English), 60(5), 2594–2598. https://doi.org/10.1002/anie.202009842

• PMID 33441565 - A DNA origami-based aptamer nanoarray for potent and reversible anticoagulation in hemodialysis

  • Zhao, S., Tian, R., Wu, J., Liu, S., Wang, Y., Wen, M., Shang, Y., Liu, Q., Li, Y., Guo, Y., Wang, Z., Wang, T., Zhao, Y., Zhao, H., Cao, H., Su, Y., Sun, J., Jiang, Q., & Ding, B. (2021). A DNA origami-based aptamer nanoarray for potent and reversible anticoagulation in hemodialysis. Nature Communications, 12(1), 358. https://doi.org/10.1038/s41467-020-20638-7

• PMID 34019379 - Clustering of death receptor for apoptosis using nanoscale patterns of peptides

  • Wang, Y., Baars, I., Fördös, F., & Högberg, B. (2021). Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides. ACS Nano, 15(6), 9614–9626. https://doi.org/10.1021/acsnano.0c10104

• PMID 34096116 - DNA origami penetration in cell spheroid tissue models is enhanced by wireframe design

  • Wang, Y., Benson, E., Fördős, F., Lolaico, M., Baars, I., Fang, T., Teixeira, A. I., & Högberg, B. (2021). DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design. Advanced Materials (Deerfield Beach, Fla.), 33(29), e2008457. https://doi.org/10.1002/adma.202008457

• PMID 34723467 - A DNA nanoraft-based cytokine delivery platform for alleviation of acute kidney injury

  • Li, W., Wang, C., Lv, H., Wang, Z., Zhao, M., Liu, S., Gou, L., Zhou, Y., Li, J., Zhang, J., Li, L., Wang, Y., Lou, P., Wu, L., Zhou, L., Chen, Y., Lu, Y., Cheng, J., Han, Y.-P., … Berggren, P.-O. (2021). A DNA Nanoraft-Based Cytokine Delivery Platform for Alleviation of Acute Kidney Injury. ACS Nano, 15(11), 18237–18249. https://doi.org/10.1021/acsnano.1c07270

• PMID 35561059 - DNA kirigami driven by polymerase-triggered strand displacement

  • Chen, K., Xu, F., Hu, Y., Yan, H., & Pan, L. (2022). DNA Kirigami Driven by Polymerase-Triggered Strand Displacement. Small (Weinheim an Der Bergstrasse, Germany), 18(24), e2201478. https://doi.org/10.1002/smll.202201478

• PMID 35737584 - DNA origami-based single-molecule CRISPR machines for spatially resolved searching

  • Hao, Y., Li, M., Zhang, Q., Shi, J., Li, J., Li, Q., Fan, C., & Wang, F. (2022). DNA Origami-Based Single-Molecule CRISPR Machines for Spatially Resolved Searching. Angewandte Chemie (International Ed. in English), 61(34), e202205460. https://doi.org/10.1002/anie.202205460

• PMID 35867518 - Design of uracil-modified DNA nanotubes for targeted drug release via DNA-modifying enzyme reactions

  • Deng, Y., Tan, Y., Zhang, Y., Zhang, L., Zhang, C., Ke, Y., & Su, X. (2022). Design of Uracil-Modified DNA Nanotubes for Targeted Drug Release via DNA-Modifying Enzyme Reactions. ACS Applied Materials & Interfaces, 14(30), 34470–34479. https://doi.org/10.1021/acsami.2c09488

• PMID 35917300 - DNA origami as a nanomedicine for targeted rheumatoid arthritis therapy through reactive oxygen species and nitric oxide scavenging

  • Ma, Y., Lu, Z., Jia, B., Shi, Y., Dong, J., Jiang, S., & Li, Z. (2022). DNA Origami as a Nanomedicine for Targeted Rheumatoid Arthritis Therapy through Reactive Oxygen Species and Nitric Oxide Scavenging. ACS Nano, 16(8), 12520–12531. https://doi.org/10.1021/acsnano.2c03991

• PMID 35973129 - ATP-responsive strand displacement coupling with DNA origami/AuNPs strategy for the determination of microcystin-LR using surface-enhanced Raman spectroscopy

  • Huo, B., Xia, L., Gao, Z., Li, G., & Hu, Y. (2022). ATP-Responsive Strand Displacement Coupling with DNA Origami/AuNPs Strategy for the Determination of Microcystin-LR Using Surface-Enhanced Raman Spectroscopy. Analytical Chemistry, 94(34), 11889–11897. https://doi.org/10.1021/acs.analchem.2c02440

• PMID 35980981 - Coarse-grained simulations for the characterization and optimization of hybrid protein-DNA nanostructures

  • Narayanan, R. P., Procyk, J., Nandi, P., Prasad, A., Xu, Y., Poppleton, E., Williams, D., Zhang, F., Yan, H., Chiu, P.-L., Stephanopoulos, N., & Šulc, P. (2022). Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein–DNA Nanostructures. ACS Nano, 16(9), 14086–14096. https://doi.org/10.1021/acsnano.2c04013

• PMID 36459554 - DNA origami-based artificial antigen-presenting cells for adoptive T cell therapy

  • Sun, Y., Sun, J., Xiao, M., Lai, W., Li, L., Fan, C., & Pei, H. (2022). DNA origami-based artificial antigen-presenting cells for adoptive T cell therapy. Science Advances, 8(48), eadd1106. https://doi.org/10.1126/sciadv.add1106

• PMID 36917482 - Selective recognition of the amyloid marker single thioflavin T using DNA origami-based gold nanobipyramid nanoantennas

  • Kaur, C., Kaur, V., Rai, S., Sharma, M., & Sen, T. (2023). Selective recognition of the amyloid marker single thioflavin T using DNA origami-based gold nanobipyramid nanoantennas. Nanoscale, 15(13), 617–6178. https://doi.org/10.1039/d2nr06389a

List of Other caDNAno Designs

• Transfoldable DNA origami Miura folding technique-based structures from Tohoku University's Team Sendai during BIOMOD 2018
  • Tohoku University, Molecular Robotics Laboratory (2018). DNA Transfolder: Team Sendai 2018 - Miura Folding. DNA Transfolder | Team Sendai 2018. https://biomodteamsendai2018.bitbucket.io/wiki/index.html
• Practice designs for very commonly used structures that are used as references. This includes a triangle, tetrahedron, bowtie, and Rothemund's rectangle.
  • Rothemund P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297–302. https://doi.org/10.1038/nature04586

Citation of caDNAno

This repository would not be possible without the help of Shawn Douglas and his lab at UCSF, who created such a fundamental piece of software used for DNA origami structural designing. The following is the citation to caDNAno. All designs in this repository use the 2nd version of caDNAno, which is currently still being updated as of this readme post.

• Douglas, S. M., Marblestone, A. H., Teerapittayanon, S., Vazquez, A., Church, G. M., & Shih, W. M. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15), 5001–5006. https://doi.org/10.1093/nar/gkp436