Article
Chemistry, Multidisciplinary
Jianhua Wang, Yuhui Wei, Ping Zhang, Yue Wang, Qinglin Xia, Xiaoguo Liu, Shihua Luo, Jiye Shi, Jun Hu, Chunhai Fan, Bin Li, Lihua Wang, Xingfei Zhou, Jiang Li
Summary: In this study, the folding processes of several multidomain DNA origami structures were visualized using atomic force microscopy under ambient annealing conditions in solution, revealing the coexistence of diverse transitional structures that might result in the same prescribed products. Based on experimental observations and energy landscape simulations, the heterogeneity of the folding pathways of multidomain DNA origami structures was proposed.
Article
Chemistry, Multidisciplinary
Jiajia Zou, Ashley C. Stammers, Andrea Taladriz-Sender, Jamie M. Withers, Iain Christie, Marina Santana Vega, Badri L. Aekbote, William J. Peveler, David A. Rusling, Glenn A. Burley, Alasdair W. Clark
Summary: An orthogonal, noncovalent approach is presented for the assembly of higher-order DNA origami nanostructures. By incorporating perfluorinated tags into DNA origami tiles, their hierarchical assembly is controlled via fluorous-directed recognition. This integrated catch-and-latch approach combining fluorous effect with base-pairing specificity enables increased assembly efficiency and requires fewer DNA sequences, providing a cheap and efficient means for producing discrete superstructures in DNA nanotechnology.
Article
Chemistry, Multidisciplinary
Yuxiang Dong, Jiliang Liu, Xuanzhao Lu, Jialin Duan, Liqi Zhou, Lizhi Dai, Min Ji, Ningning Ma, Yong Wang, Peng Wang, Jun-Jie Zhu, Qianhao Min, Oleg Gang, Ye Tian
Summary: Self-assembly processes are important for fabricating complexly organized nanomaterials, but often limited in creating structures with multiscale order. In this study, a two-stage assembly strategy is introduced to successfully form complexly organized nanoparticle crystals.
Article
Multidisciplinary Sciences
Oliver G. Hayes, Benjamin E. Partridge, Chad A. Mirkin
Summary: This study demonstrates the deliberate control of hierarchical assembly of protein-DNA materials by exploiting the chemical anisotropy of proteins and the programmability of DNA ligands. The introduction of orthogonal DNA interactions with disparate strengths onto specific geometric regions of a model protein leads to directional assembly and increased multi valency through DNA sequence design. The judicious DNA design not only directs assembly along a specific pathway but also influences distinct structural outcomes from a single pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Shuang Wang, Xiaolin Xie, Zhi Chen, Ningning Ma, Xue Zhang, Kai Li, Chao Teng, Yonggang Ke, Ye Tian
Summary: The DNA-grafted nanoparticle serves as a programmable atom equivalent for assembling three-dimensional superlattice with novel properties, allowing for the exploration of assembly strategies and mechanisms, as well as future applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Multidisciplinary
John R. Jungck, Stephen Brittain, Donald Plante, James Flynn
Summary: The researchers have discovered three new hybrid classes based on their experience with 4D printing, indicating that self-assembly can involve self-folding, environment-dependent folding, and chaotic alternating processes. By using geometric and topological perspectives, they have developed design principles and tested them through experiments and models to demonstrate five different processes.
Article
Chemistry, Multidisciplinary
Ruixin Li, Haorong Chen, Jong Hyun Choi
Summary: Deployable geometries are finite auxetic structures that can maintain their overall shape while expanding and contracting. A deployable flight ring made from DNA origami has been demonstrated in this study, showing the feasibility of deployable nanostructures. The flight ring consists of six triangles in two layers that can switch between open and closed states, with a trefoil knot topology and negative Poisson's ratios. This work provides a versatile platform for topological studies and opens up new opportunities for bioengineering.
Article
Nanoscience & Nanotechnology
Esra Oktay, Joshua Bush, Merlyn Vargas, Dylan Valerio Scarton, Bailey O'Shea, Amber Hartman, Christopher M. Green, Kayla Neyra, Carolina M. Gomes, Igor L. Medintz, Divita Mathur, Remi Veneziano
Summary: Functional DNA origami nanoparticles (DNA-NPs) are used as nanocarriers in biomedical applications. A simple and robust strategy based on asymmetric polymerase chain reaction (aPCR) allows direct synthesis of custom-length scaffolds that can be randomly or precisely modified.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Jingwen Wang, Junjie Yuan, Jiajia Liu, Haixia Zou, Lin Yang, Hong Chen, Xiangmeng Qu
Summary: DNA self-assembly is a promising method for constructing complex nanostructures. However, the current approach requires separate design and professional operation, limiting its development and application. In this study, a novel point-and-shoot strategy based on enzyme-assisted DNA paper-cutting was proposed to construct planar DNA nanostructures using the same DNA origami as a template. By annealing the long scaffold strand and selected staple strands, planar DNA nanostructures were successfully constructed. This strategy overcomes the complexity limitation of planar DNA nanostructures and simplifies the design and operation process. Overall, this strategy shows great potential for manufacturing DNA nanostructures.
Article
Chemistry, Multidisciplinary
Michael Scheckenbach, Tom Schubert, Carsten Forthmann, Viktorija Glembockyte, Philip Tinnefeld
Summary: Advancements in DNA nanotechnology and DNA origami techniques have enabled the easy design and synthesis of complex and functional nanostructures. Molecular devices are prone to rapid degradation, so self-repair mechanisms are desirable. By utilizing the self-assembly and reconfigurability of DNA origami nanostructures, self-repair of defects can be induced.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Aleksandra K. Adamczyk, Teun A. P. M. Huijben, Miguel Sison, Andrea Di Luca, Stefano Vanni, Sophie Brasselet, Kim I. Mortensen, Fernando D. Stefani, Mauricio Pilo-Pais, Guillermo P. Acuna
Summary: This study demonstrates a controlled orientation of single molecules in DNA origami by linking them to oligonucleotide strands and leaving unpaired bases. The number of unpaired bases affects the stretching and orientation of the fluorophore linkers. These findings expand the application of DNA origami in the fabrication of nanodevices involving orientation-dependent molecular interactions.
Article
Chemistry, Multidisciplinary
Shuoxing Jiang, Nibedita Pal, Fan Hong, Nour Eddine Fahmi, Huiyu Hu, Matthew Vrbanac, Hao Yan, Nils G. Walter, Yan Liu
Summary: Controlling the nucleation step of a self-assembly system is crucial for engineering structural complexity and dynamic behaviors. This study investigates the inherent dynamics of three general nucleation modes in DNA tile-based self-assembly and reveals temperature-dependent kinetics and a nucleation-growth model are key factors. The assembly of tiles can be externally regulated by the hosting frame and an UV-responsive trigger, offering a general strategy for controlling the self-assembly process.
Article
Chemistry, Multidisciplinary
Willi R. Berg, Jonathan F. Berengut, Changzhuang Bai, Laura Wimberger, Lawrence K. Lee, Felix J. Rizzuto
Summary: In this study, we demonstrate a method to achieve dynamics in DNA nanostructures without DNA modification. By using protonated DNA strands and a small molecule pH regulator, we successfully assemble DNA origami into one-dimensional fibrils, which can be reversibly assembled and disassembled by visible light activation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Erik Benson, Rafael Carrascosa Marzo, Jonathan Bath, Andrew J. Turberfield
Summary: Linear actuators based on DNA origami are demonstrated in this paper, providing nanoscale precision through bottom-up assembly at the molecular scale. Two assembly strategies and two positioning strategies are used to control the position of the slider on the rail with high yield and precision. These components have potential applications in molecular machinery and nanoscale manufacture, including programmed chemical synthesis.
Article
Chemistry, Multidisciplinary
Cindy Ng, Anirban Samanta, Ole Aalund Mandrup, Emily Tsang, Sarah Youssef, Lasse Hyldgaard Klausen, Mingdong Dong, Minke A. D. Nijenhuis, Kurt V. Gothelf
Summary: Engineered architectural control over double-stranded DNA (dsDNA) is challenging, but the triplex origami methodology provides a solution. Triplex-forming oligonucleotides (TFOs) are used to bind purines in dsDNA and compact it into well-defined objects with various structural features. The methodology allows for modulating the length of integrated and free-standing dsDNA loops with high efficiency and enables unprecedented spatial control over dsDNA templates.
ADVANCED MATERIALS
(2023)
Correction
Chemistry, Multidisciplinary
Joshua A. Johnson, Vasiliki Kolliopoulos, Carlos E. Castro
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Will T. Kaufhold, Wolfgang Pfeifer, Carlos E. Castro, Lorenzo Di Michele
Summary: The study utilizes metadynamics to sample the free energy landscapes of DNA nanostructures and demonstrates its ability to predict the mechanical response of DNA nanodevices. These findings are significant for the design and application of DNA nanostructures.
Article
Chemistry, Multidisciplinary
Michael Darcy, Kyle Crocker, Yuchen Wang, Jenny Le, Golbarg Mohammadiroozbahani, Mahmoud A. S. Abdelhamid, Timothy D. Craggs, Carlos E. Castro, Ralf Bundschuh, Michael G. Poirier
Summary: The ability to apply and measure high forces on the nanometer scale is crucial for the development of nanomedicine, molecular robotics, and understanding biological processes. Current force spectroscopy techniques have limitations in applying forces in constrained geometries. DNA-based molecular calipers have shown promise as an alternative, but their force application capabilities are currently limited. This study implemented DNA origami nanocalipers with tunable mechanical properties to demonstrate the ability to apply forces of at least 20 piconewtons with a nanometer-scale dynamic range.
Article
Electrochemistry
Xiaoqin Wang, Kaden C. Stevens, Jeffrey M. Ting, Alexander E. Marras, Gelareh Rezvan, Xiaojun Wei, Nader Taheri-Qazvini, Matthew Tirrell, Chang Liu
Summary: In this study, the potential of diblock synthetic polyelectrolytes as nanopore sensing probes was explored by investigating their translocation behaviors through alpha-hemolysin and MspA nanopores. The results indicate efficient translocations of PEO-b-PSS through alpha-HL and PEO-b-PVBTMA through MspA, suggesting that synthetic polyelectrolytes can offer more flexibility and cost-effectiveness for nanopore sensing.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
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
Summary: The study demonstrates that DNA origami (DO) nanotechnology can be used to construct precise nanostructures capable of functionalization and has a wide range of biomedical applications. DO structures distribute well systemically, eliciting a gradually diminishing mild pro-inflammatory response, while being non-toxic.
Article
Biotechnology & Applied Microbiology
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
Summary: By using single-stranded DNA HDR templates with reduced toxicity and small-molecule combinations, the efficiency of CRISPR-mediated site-specific transgene insertion can be greatly enhanced. This method is applicable to various target loci, knock-in constructs, and primary human cell types, with high HDR efficiencies. Furthermore, it can be applied in pathogenic gene variant modeling, gene-replacement strategies, and nonviral chimeric antigen receptor-T cell manufacturing with improved knock-in efficiencies and yields.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Diogenes G. da S. Fernandes, Graziella S. Capo, Aryane Tofanello, Carlos E. Castro, Bruno B. Foltran, Fabio M. Squina, Maria H. C. Santos, Romerio R. S. Silva, Claudener S. Teixeira, Wanius Garcia
Summary: This study reports the synthesis of silver/silver chloride nanoparticles (NPs) assisted by ConA and DVL. The NPs showed interactions with membrane carbohydrates and potential applications in selective recognition and biotechnological applications.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Anjelica Kucinic, Chao-Min Huang, Jingyuan Wang, Hai-Jun Su, Carlos E. Castro
Summary: Structural DNA nanotechnology enables the design of complex nanoscale structures with programmable properties. Researchers developed a multi-component DNA origami 6-bar mechanism that can be reconfigured into various shapes, providing potential applications in biosensing and materials with tunable properties.
Article
Chemistry, Multidisciplinary
Yuchen Wang, Sebastian Sensale, Miguel Pedrozo, Chao-Min Huang, Michael G. Poirier, Gaurav Arya, Carlos E. Castro
Summary: Biomolecular nanotechnology is used to mimic robotic capabilities in nanoscale systems, and DNA origami is an attractive method for creating complex nanorobotic devices. This study introduces a communication mechanism inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. The research demonstrates that one arm can regulate the motion range and conformational state of the distal arm, and signal transmission can be modulated by tuning thermal fluctuations and controlling the conformational states of the components.
Article
Chemistry, Multidisciplinary
Yuchen Wang, Anjelica Kucinic, Lilly Des Rosiers, Peter E. Beshay, Nicholas Wile, Michael W. Hudoba, Carlos E. Castro
Summary: DNA origami nanotechnology has potential for diverse applications, but its use in education is limited due to high cost and time requirements. We developed an experiment module for classroom implementation, focusing on a deformable hinge joint, that can be evaluated within 120 minutes using cost-effective equipment. Two beam-based models were presented to describe the joint deformation. This module can broaden access to and interest in the mechanical design of DNA origami.
APPLIED SCIENCES-BASEL
(2023)
Proceedings Paper
Engineering, Electrical & Electronic
Yanyu Xiong, Qinglan Huang, Taylor D. Canady, Priyash Barya, Shengyan Liu, Opeyemi H. Arogundade, Caitlin M. Race, Congnyu Che, Xiaojing Wang, Lifeng Zhou, Anh Igarashi, Xing Wang, Manish Kohli, Andrew M. Smith, Brian T. Cunningham
Summary: In this study, the signal of nanoscale quantum emitters was significantly boosted using the multiplicative effects of amplified excitation, highly directed extraction, Purcell enhancement, and blinking suppression on a photonic crystal surface. The platform achieved single quantum dot sensitivity with high signal-to-noise ratio, and ultrasensitive detection with a wide linear dose-response range.
Review
Materials Science, Multidisciplinary
Alexander E. Marras
Summary: The programmability of geometric, mechanical, and dynamic properties in DNA nanotechnology has led to its rapid growth and impressive library of nanoscale structures and devices. This review explores the challenge of expanding DNA technology to larger scales by hierarchical assembly using DNA base pairing, base stacking interactions, and DNA-peptide conjugates, and provides examples of their functional applications.
MRS COMMUNICATIONS
(2022)
Proceedings Paper
Engineering, Biomedical
Neha Chauhan, Weijing Wang, Han Keun Lee, Yanyu Xiong, Tianyi Zhang, Nicholas Magazine, Lu Peng, Lifeng Zhou, Weishan Huang, Xing Wang, Brian T. Cunningham
Summary: A novel approach using a Designer DNA Nanostructure (DDN) mixed with saliva has been developed for rapid self-testing of SARS-CoV-2. This low-cost and convenient technology can detect virus concentration in a short time period. It can be wirelessly managed with a smartphone and has the potential for contact tracing and interaction with health services.
SMART BIOMEDICAL AND PHYSIOLOGICAL SENSOR TECHNOLOGY XIX
(2022)
Article
Biochemistry & Molecular Biology
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
Summary: DNA nanostructures are a promising tool for delivering molecular payloads to cells, but effectively delivering genetic material to the nucleus has been a challenge. This study successfully integrated gene material into cells using DNA nanostructures as HDR templates, with increased entry into the nucleus through CRISPR technology. These nanostructured templates showed lower toxicity and higher insertion efficiency compared to unstructured DNA templates.
NUCLEIC ACIDS RESEARCH
(2022)