Nanoengineering and Biodesign Laboratory: Publications
Full list of publications here: google scholar
Publications
- *Roozbahani, G., *Colosi, P., *Oravecz, A., Sorokina, E.M., Pfeifer, W., Shokri, S., Wei, Y., Didier, P., DeLuca, M., Arya, G., *Tora, L., *Lakadamyali, M., *Poirier, M.G., *Castro, C.E., Piggybacking functionalized DNA nanostructures into live cell nuclei, submitted (preprint on bioRxiv, https://doi.org/10.1101/2023.12.30.573746)
- Teng, T., Bernal-Chanchavac, J., Stephanopoulos, N., Castro, C.E. Construction of reconfigurable and polymorphic DNA origami assemblies with coiled-coil patches and patterns. Advanced Science, Accepted (2024) (preprint on bioRxiv, https://doi.org/10.1101/2023.09.23.559112)
- Yuchen Wang, Xin Jin, Carlos E Castro, Accelerating the Characterization of Dynamic DNA Origami Devices with Deep Neural Networks. Scientific Reports, 13: 15196 (2023), https://doi.org/10.1038/s41598-023-41459-w , preprint on bioRxiv, https://www.biorxiv.org/content/10.1101/2023.05.11.540408v1
- *Wolfgang G Pfeifer, *Chao-Min Huang, Michael G Poirier, *Gaurav Arya, G., Carlos E Castro, Versatile Computer Aided Design of Freeform DNA nanostructures and assemblies. Science Advances, Accepted, https://doi.org/10.1126/sciadv.adi0697, preprint on bioRxiv https://www.biorxiv.org/content/10.1101/2023.03.30.535006v1
- Marcello DeLuca, M., Wolfgang G Pfeifer, Chao-Min Huang, Michael G Poirier, Carlos E Castro, Gaurav Arya, Thermally Reversible Pattern Formation in Arrays of Molecular Rotors. Nanoscale,15:8356-8365, https://doi.org/10.1039/D2NR05813H, preprint on bioRxiv https://www.biorxiv.org/content/10.1101/2022.10.19.512893v1
- *Yuchen Wang, *Sebastian Sensale, *Miguel Pedrozo, Michal G. Poirier, Gaurav Arya, Carlos E Castro, Steric Communication between Dynamic Components on DNA nanodevices, ACS Nano, 17(9): 8271–8280 https://doi.org/10.1021/acsnano.2c12455, preprint on bioRxiv https://www.biorxiv.org/content/10.1101/2022.12.15.520588v1
- *Peter E Beshay, *Anjelica Kucinic, A., Wile, N., Patrick D Halley, Lilly Des Rosiers, Amjad Chowdhury, Julia L Hall, *Carlos E Castro, *Michael W Hudoba, Translating DNA origami Nanotechnology to Middle School, High School, and Undergraduate Laboratories. The Biophysicist, https://doi.org/10.35459/tbp.2022.000228 (2023), preprint on bioRxiv, https://www.biorxiv.org/content/10.1101/2022.09.15.508130v1
- *Yuchen Wang, *Anjelica Kucinic, Lilly Des Rosiers, Nick Wile, *Michael W Hudoba, *Carlos E Castro, Mechanical Design of DNA Origami in the Classroom. Applied Sciences, 13(5): 3208 (2023)
- Anjelica Kucinic, Chao-Min Huang, Jingyuan Wang, Hai-Jun Su, Carlos E Castro. DNA origami tubes with reconfigurable cross-sections. Nanoscale, 2(15): 562-572 (2022)
- Melika Shahhosseini, Peter E. Beshay, Ehsan Akbari, Niksa Roki, Christopher R. Lucas, Alex Avendano, Jonathan W. Song*, and Carlos E. Castro . Multiplexed Detection of Molecular Interactions with DNA Origami Engineered Cells in 3-D Collagen Matrices. ACS Applied Materials and Interfaces, 14(50):55307–55319 (2022), preprint on bioRxiv (https://www.biorxiv.org/content/10.1101/2022.02.04.479158v1
- Ehsan Akbari, Melika Shahhosseini, Ariel Robbins, Michael G Poirier, Jonathan W Song, Carlos E Castro, Low cost and massively parallel force spectroscopy with fluid loading on a chip, Nat. Communications, 2022
- Brian R Shy, Vivasvan S Vykunta, Alvin Ha, Alexis Talbot, Theodore L Roth, David N Nguyen, Wolfgang G Pfeifer, Yan Yi Chen, Franziska Blaeschke, Eric Shifrut, Shane Vedova, Murad R Mamedov, Jing-Yi Jing Chung, Hong Li, Ruby Yu, David Wu, Jeffrey Wolf, Thomas G Martin, Carlos E Castro, Lumeng Ye, Jonathan H Esensten, Justin Eyquem, Alexander Marson, High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails, Nat. Biotechnology, 2022
- Carlos Castro, Design of DNA based dynamic devices, assemblies, and composites, Novel Patterning Technologies, 2022
- Christopher R Lucas, Patrick D Halley, Amjad A Chowdury, Bonnie K Harrington, Larry Beaver, Rosa Lapalombella, Amy J Johnson, Erin K Hertlein, Mitch A Phelps, John C Byrd, Carlos E Castro, DNA Origami Nanostructures Elicit Dose‐Dependent Immunogenicity and Are Nontoxic up to High Doses In Vivo, Small, 2022
- Melika Shahhosseini, Anjelica Kucinic, Peter Beshay, Wolfgang Pfeifer, Carlos Castro,
Dynamic and Mechanical Applications of DNA Nanostructures in Biophysics, DNA Origami: Structures, Technology, and Applications, 2022 - Michael Darcy, Kyle Crocker, Yuchen Wang, Jenny V Le, Golbarg Mohammadiroozbahani, Mahmoud AS Abdelhamid, Timothy D Craggs, Carlos E Castro, Ralf Bundschuh, Michael G Poirier, High-Force Application by a Nanoscale DNA Force Spectrometer, ACS Nano, 2022
- Enrique Lin-Shiao, Wolfgang G Pfeifer, Brian R Shy, Mohammad Saffari Doost, Evelyn Chen, Vivasvan S Vykunta, Jennifer R Hamilton, Elizabeth C Stahl, Diana M Lopez, Cindy R Sandoval Espinoza, Alexander E Deyanov, Rachel J Lew, Michael G Poirer, Alexander Marson, Carlos E Castro, Jennifer A Doudna, CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells, Nucleic acids research, 2022
- PD Halley, CR Lucas, N Roki, NJ Vantangoli, KP Chenoweth, CE Castro, DNA Origami Nanodevices for Therapeutic Delivery Applications, Biotechnologies for Gene Therapy, 2022
- Kaufhold, W.T., Pfeifer, W.G., Castro, C.E., Di Michele, L. Probing the mechanical properties of DNA nanostructures with metadynamics. (under review, preprint on arXiv: https://arxiv.org/abs/2110.01477)
- Darcy, M., Crocker, K., Wang, Y., Le, J., Mohommadiroozbahani, G., Abdelhamid, M., Craggs, T., Castro, C.E., Bundschuh, R., Poirier, M. High Force Application by a Nanoscale DNA Force Spectrometer. ACS Nano, Accepted (2022)
- Shy, B.R., Vykunta, V.S., Ha, A., Talbot, A., Roth, T.L., Nguyen, D.N., Pfeifer, W.G., Chen, Y.Y., Blaeschke, F., Shifrut, E., Vedova, S., Mamedov, M.R., Chung, J.-Y., Li, H., Wolf, J., Martin, T.G., Castro, C.E., Ye, L., Esensten, J.H., Eyquem, J., Marson, A.* Hybrid ssDNA repair templates enable high yield genome engineering in primary cells for disease modeling and cell therapy manufacturing. Nature Biotechnology, Accepted (2022)
- Lin-Shiao, E., Pfeifer, W., Shy, B., Saffari Doost, M., Chen, E., Vykunta, V., Hamilton, J., Stahl, ., **Lopez, D., Sandoval Espinoza, C., Dejanov, A., Lew, R., Poirer, M., Marson, A., Castro, C.E., Doudna, J.A. CRISPR-Cas9 mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Nucleic Acids Research, 50(3): 1256-1268 (2022) (preprint on bioRxiv: https://www.biorxiv.org/content/10.1101/2021.11.08.467750v1)
- Crocker, K., **Johnson, J.A., Pfeifer, W.G., Castro, C.E., Bundschuh, R.A. A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior. Nanoscale, 13: 13746-13757 (2021)
- **,+Wang, Y., **,+Le, J.V., Crocker, K., **Andrioff, N.R., Croy, C.M., Poirier, M.G., Bundschuh, R.A., Castro, C.E. A Nanoscale DNA Force Spectrometer Capable of Applying Tension and Compression on Biomolecules. Nucleic Acids Research, 49(15): 8987–8999 (2021)
- **Huang, C.M., **Kucinic, A., **Johnson, J.A., Su, H.-J.*, and Castro, C.E.*, Integrated computer-aided engineering and design for DNA assemblies. Nature Materials, https://doi.org/10.1038/s41563-021-00978-5 (2021)
- **Johnson, J.A., **Kolliopoulos, V., Castro, C.E. Co-self-assembly of multiple DNA origami nanostructures in a single pot. Chemical Communications, 57:4795-4798 (2021)
- Arroyo-Currás N., Sadeia, M., Ng, A.K., Fyodorova, Y., Williams, N., Afif, T., Huang, C.-M., Ogden, N., Andresen Eguiluz, R.C., Su, H.-J., Castro, C.E., Plaxco, K.W., Lukeman, P.S. An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets. Nanoscale, 12:13907-13911 (2020)
- Asghari Adib, A., Sheikhi, A., **Shahhosseini, M., Simeunovic, A., Wu, S., Castro, C.E., Zhao, R., Khademhosseini, A., Hoelzle, D. Direct-write 3D printing and characterization of a GelMA-based biomaterial for intracorporeal tissue engineering. Biofabrication, 12(4): 045006 (2020)
- DeLuca, M., Shi, Z., Castro, C.E., Arya, G. Dynamic DNA Nanotechnology: Toward Functional Nanoscale Devices. Nanoscale Horizons, 5, 182-201 (2020)
- Emily M. McWilliams, Christopher R. Lucas, Timothy Chen, Bonnie K. Harrington, Ronni Wasmuth, Amanda Campbell, Kerry A. Rogers, Carolyn M. Cheney, Xiaokui Mo, Leslie A. Andritsos, Farrukh T. Awan, Jennifer Woyach, William E. Carson III,Jonathan Butchar, Susheela Tridandapani, Erin Hertlein, Carlos E. Castro, Natarajan Muthusamy, and John C. Byrd, "Anti-BAFF-R Antibody VAY-736 Demonstrates Promising Pre-Clinical Activity in CLL and Enhances Effectiveness of Ibrutinib." Blood Advances. (2019) Accepted
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Halley, P.D., Patton, R.A., Chowdhury, A., Byrd, J.C., Castro, C.E., "Low-cost, simple, and scalable self-assembly of DNA origami nanostructures." in revision
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Zhao, D., Le, J., Darcy, M., Poirier, M.G., Castro, C.E., Bundschuh, R., "Quantitative Modeling of Concomitant Nucleosome Unwrapping." in revision
- Ke, Y., Castro, C.E., Choi, J.H., "Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research." Annual Review of Biomedical Engineering. (2018) link
- Huang, C.M., Kucinic, A., Le, J.V., Castro, C.E.,* and Su, H.-J.,* "Uncertainty Quantification of a DNA Origami Mechanism Using a Coarse-Grained Model and Kinematic Variance Analysis." Nanoscale. (2018) link
- Zhou, L., Marras, A.E., Huang, C-M., Castro, C.E.,* Su, H-J.,* "Paper origami-inspred Design and Actuation of DNA Nanorobots with Complex Motions." Small. (2018) link
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Marras, A.E., Shi, Ze, Lindell, M., Zhou, L., Su, H-J., Arya, G.,* Castro, C.E.,* "Cation-activated avidity for rapid reconfiguration of DNA nanodevices." ACS Nano. (2018). link
- Lauback, S., Mattioli, K.R., Marras, A.E., Armstrong, M., Rudibaugh, T., Sooryakumar, R.,* Castro, C.E.,* "Real-time Magnetic Control of DNA Nanodevices." Nature Communications. link
- Lei, D., Marras, A.E., Liu, J., Huang, C-M., Zhou, L., Castro, C.E., Su, H-J., Ren, G., "3D Structural Dynamics of DNA origami Mechanisms and Machines Using Individual Particle Electron Tomography." Nature Communications. link
- Wang, P., Chatterjee, G., Yan, H., LaBean, T.H., Turberfield, A.J., Castro, C.E., Seelig, G., and Ke, Y. Practical aspects of structural and dynamic DNA nanotechnology. MRS Bulletin. link
- Castro,C.E., Dietz, H., Högberg, B. DNA origami devices for molecular-scale precision measurements. MRS Bulletin. link
- Akbari, E., Mollica, M., Lucas, C.R., Bushman, S., Patton, R.A., Shahhosseini, M., Song, J.W., Castro, C.E., "Engineering Cell Surface Function with DNA Origami." Advanced Materials. link
- Hudoba, M., Luo, Y., Zacharias, A., Poirier, M.G., Castro, C.E., "A Dynamic DNA origami device for measuring compressive depletion forces." ACS Nano. link
- Shi, Z., Castro, C.E., Arya, G. "Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations." ACS Nano link
- Zhou, L., Su, H-J., Marras, C-M., Castro, C.E., "Projection kinematic analysis of DNA origami mechanisms based on a two-dimensional TEM image." Mechanisms and Machine Theory. link
- Liang, B., Nagarajan, A., Hudoba, M.W., Alvarez, R., Castro, C.E., Soghrati, S., "Automated Quantification of the Impact of Defects on the Mechanical Behavior of DNA Origami Nanoplates." ASME Journal of Biomechanical Engineering. link
- Le, J., Luo, Y., Darcy, M., Lucas, C.R., Goodwin, M., Poirier, M.G., Castro, C.E., "Probing Nucleosome Stability with a DNA Origami Nanocaliper." ACS Nano. link
- Marras, A.E., Zhou, L., Kolliopoulos, V., Su, H., Castro, C.E., "Directing folding pathways for multi-component DNA origami nanostructures with complex topology." New Journal of Physics. link
- Kearney, C.J., Lucas, C.R., O’Brien, F.J., Castro, C.E., "DNA Origami: Folded DNA-Nanodevices That Can Direct and Interpret Cell Behavior." Advanced Materials. link
- Halley, P.D.*, Lucas, C.R.*, McWilliams, E.M., Webber, M.J., Patton, R., Kural, C., Lucas, D.M., Byrd, J.C., Castro, C.E. "Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug Resistance Mechanisms in a Leukemia Model." Small. link (*co-first author)
- Zhou, L., Marras, A.E., Castro, C.E., Su, H. "Design and Modeling of Compliant DNA Origami Mechanisms." Journal of Mechanisms and Robotics. link
- Zhou, L., Marras, A.E., Su, H., Castro, C.E. "Direct design of an energy landscape with bistable DNA origami mechanisms." Nano Letters. link
- Castro, C.E., Su, H., Marras, A.E., Zhou, L., Johnson, J. "Mechanical Design of DNA nanostructures." Nanoscale. link
- Marras, A.E., Zhou, L., Su, H., Castro, C.E. "Programmable motion of DNA origami mechanisms." Proceedings of the National Academy of Sciences. link (pdf)
- Gupta, C., Liao, W. C., Gallego-Perez, D., Castro, C. E., & Lee, L. J. "DNA translocation through short nanofluidic channels under asymmetric pulsed electric field." Biomicrofluidics. link
- Zhou, L., Marras, A.E., Su, H., Castro, C.E. "DNA origami compliant nanostructures with tunable mechanical properties." ACS Nano. link
- Wu, Y., Kwak, K.J., Agarwal, K., Marras, A.E., Wang, C., Mao, Y, Huang, X., Ma, J., Yu, B., Lee, R. Vachani, A., Marcucci, G., Byrd, J., Muthusamy, N., Otterson, G., Huang, K., Castro, C.E., Paulaitis, M., Nano-Sinkam, S.P., Lee, L.J., "Detection of Extracellular RNAs in Cancer and Viral Infection via Tethered Cationic Lipoplex Nanoparticles Containing Molecular Beacons." Analytical Chemistry. link
- Nguyen, V., Lilly, B., Castro, C.E. "The exoskeletal structure and tensile loading behavior of an ant neck joint." Journal of Biomechanics. link (pdf)
- Marras, A.E., Su, J., Castro, C. E. Design of DNA Origami Machines and Mechanisms. ASME International Mechanical Engineering Congress and Exposition (IMECE 2012), Houston, Texas, Nov 9-15
- Su, H., Castro, C.E., Marras, A.E., Hudoba, M. Design and Fabrication of DNA Origami Mechanisms and Machines. Second ASME/IEE International Conference on Reconfigurable Mechanisms and Robots (ReMAR 2012), Tianjin, China, July 9-11, 2012
- Castro, C.E., Kilchherr F., Kim, D., Lin Shiao, E., Wauer, T., Wortmann, P., Bathe, M., Dietz, HA, "Primer to Scaffolded DNA Origami." Nature Methods. link
- Castro, C.E., Dong, J., Lindquist, S., Boyce, M.C., Lang, M.J., "Physical Properties of Polymorphic Prion Proteins." Biophysical Journal
- Jungmann, R., Scheible, M., Kuzyk, A., Pardatscher, G., Castro, C.E., and Simmel F.C., "DNA origami-based nanoribbons: assembly, length distribution, and twist." Nanotechnology
- Wang, L., Castro, C.E., and Boyce, M.C. Growth strain-induced membrane morphology of white blood cells. Soft Matter. 7:11319-11324 (2011)
- Tam, J.M., Castro, C.E., Heath, R.J., Mansour, M.K., Cardenas, M.L., Xavier, R., Lang, M.J., Vyas, J.M. (2011) Use of an Optical Trap for Study of Host-Pathogen Interactions for Dynamic Live Cell Imaging J Vis Exp; http://www.jove.com/details.stp?id=3123 doi: 10.3791/3123.
- Tam, J., Castro, C.E., Heatsh, R.J., Cardenas, M.J., Xavier, R., Lang, M.J., Vyas, J.M., "Control and Manipulation of Pathogens with an Optical Trap for Live Cell Imaging of Intercellular Interactions." PLoS One
- Dong, J., Castro, C.E., Boyce, M.C., Lang, M.J., and Lindquist, S., "Optical trapping with high forces reveals unexpected behaviors of prion fibrils." Nature Structural & Molecular Biology
- Palmer, J.S., Castro, C.E., Arslan, M., Boyce, M.C. Constitutive Models for the Force- Extension Behavior for Biological Filaments. Proceedings of the IUTAM symposium on Molecular, Cellular, and Tissue Biomechanics. IUTAM Bookseries, Volume 16
- Kim, S.T., Takeuchi, K., Zhen-Yu, J.S., Touma, M., Castro, C.E., Fahmy, A., Vibhuti, D., Kappes, D., Lang, M.J., Wagner, G., Reinherz, E., "The αβ T cell receptor is an anisotropic mechanosensor." Journal of Biological Chemistry
- Villarreal, M.G., Sánchez Peña, M.L., Castro, C.E., Castro, J.M., Cabrera-Rios, M. Using data clustering to aid the solution of multiple criteria optimization problems through data envelopment analysis, Intelligent Data Analysis – An International Journal 12(1):89-101
- Brau, R. Ferrer, J.M., Lee, H., Castro, C.E., Tam, B.K., Tarsa, P.B., Matsudaira, P, Boyce, M.C., Kamm, R.D., Lang, M.J. Passive and active microrheology with optical tweezers, Journal of Optics A: Pure and Applied Optics; 9: S103-S112
- Castro, C.E., Cabrera Rios, M., Lilly, B., Castro, J.M. Multiple Criteria Optimization with Variability Considerations in Injection Molding. Polymer Engineering and Science. 47(4):400-409