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Liu Y, Wang R, Chen Q, Chang Y, Chen Q, Fukumoto K, Wang B, Yu J, Luo C, Ma J, Chen X, Murayama Y, Umeda K, Kodera N, Harada Y, Sekine SI, Li J, Tadakuma H. Organ-Specific Gene Expression Control Using DNA Origami-Based Nanodevices. NANO LETTERS 2024. [PMID: 38920331 DOI: 10.1021/acs.nanolett.4c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Nanodevices that function in specific organs or cells are one of the ultimate goals of synthetic biology. The recent progress in DNA nanotechnology such as DNA origami has allowed us to construct nanodevices to deliver a payload (e.g., drug) to the tumor. However, delivery to specific organs remains difficult due to the fragility of the DNA nanostructure and the low targeting capability of the DNA nanostructure. Here, we constructed tough DNA origami that allowed us to encapsulate the DNA origami into lipid-based nanoparticles (LNPs) under harsh conditions (low pH), harnessing organ-specific delivery of the gene of interest (GOI). We found that DNA origami-encapsulated LNPs can increase the functionality of payload GOIs (mRNA and siRNA) inside mouse organs through the contribution from different LNP structures revealed by cryogenic electron microscope (Cryo-EM). These data should be the basis for future organ-specific gene expression control using DNA origami nanodevices.
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Affiliation(s)
- Yuxiang Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Ruixuan Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Qimingxing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Yan Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Qi Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Kodai Fukumoto
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Bingxun Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Jianchen Yu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Changfeng Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Jiayuan Ma
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
| | - Xiaoxia Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease Hangzhou, Zhejiang University School of Medicine First Affiliated Hospital, Zhejiang 310009, People's Republic of China
| | - Yuko Murayama
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yoshie Harada
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shun-Ichi Sekine
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Jianfeng Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - Hisashi Tadakuma
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210 People's Republic of China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
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Punnoose JA, Cole D, Chandrasekaran AR, Halvorsen K. Tuning the stability of DNA tetrahedra with base-stacking interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598265. [PMID: 38915531 PMCID: PMC11195101 DOI: 10.1101/2024.06.10.598265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends which contain identical base pairing interactions but different terminal stacking interactions. Testing all 16 possible combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design while retaining a common sequence in a 6-nt sticky end. This work clearly shows that stacking design influences DNA tetrahedra stability in a substantial and predictable way. The results likely apply to other types of DNA nanostructures and suggest that terminal stacking interactions play an integral role in formation and stability of DNA nanostructures.
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Wu Y, Luo L, Hao Z, Liu D. DNA-based nanostructures for RNA delivery. MEDICAL REVIEW (2021) 2024; 4:207-224. [PMID: 38919398 PMCID: PMC11195427 DOI: 10.1515/mr-2023-0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/28/2024] [Indexed: 06/27/2024]
Abstract
RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases, including cancer, genetic disorders, and infectious diseases. However, the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake. To overcome these hurdles, DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics. Due to its excellent characteristics such as programmability and biocompatibility, these DNA-based nanostructures, composed of DNA molecules assembled into precise and programmable structures, have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations. In this review, we highlight the current progress in the design and application of three DNA-based nanostructures: DNA origami, lipid-nanoparticle (LNP) technology related to frame guided assembly (FGA), and DNA hydrogel for the delivery of RNA molecules. Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.
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Affiliation(s)
- Yuanyuan Wu
- Beijing SupraCirc Biotechnology Co., Ltd, Beijing, China
| | - Liangzhi Luo
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Ziyang Hao
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Dongsheng Liu
- Department of Chemistry, Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Tsinghua University, Beijing, China
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Kou B, Wang Z, Mousavi S, Wang P, Ke Y. Dynamic Gold Nanostructures Based on DNA Self Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308862. [PMID: 38143287 DOI: 10.1002/smll.202308862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/10/2023] [Indexed: 12/26/2023]
Abstract
The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.
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Affiliation(s)
- Bo Kou
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Shikufa Mousavi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
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Posnjak G, Yin X, Butler P, Bienek O, Dass M, Lee S, Sharp ID, Liedl T. Diamond-lattice photonic crystals assembled from DNA origami. Science 2024; 384:781-785. [PMID: 38753795 PMCID: PMC7616107 DOI: 10.1126/science.adl2733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/01/2024] [Indexed: 05/18/2024]
Abstract
Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet.
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Affiliation(s)
- Gregor Posnjak
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
| | - Xin Yin
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
| | - Paul Butler
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
- Physics Department, TUM School of Natural Sciences, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
| | - Oliver Bienek
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
- Physics Department, TUM School of Natural Sciences, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
| | - Mihir Dass
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
| | - Seungwoo Lee
- Department of Integrative Energy Engineering (College of Engineering), KU-KIST Graduate School of Converging Science and Technology, Department of Biomicrosystem Technology, and KU Photonics Center, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02481, Republic of Korea
- Center for Opto-Electronic Materials and Devices, Post-Silicon Semiconductor Institute, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Ian D. Sharp
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
- Physics Department, TUM School of Natural Sciences, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
| | - Tim Liedl
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
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Ma C, Li S, Zeng Y, Lyu Y. DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications. BIOSENSORS 2024; 14:236. [PMID: 38785710 PMCID: PMC11117991 DOI: 10.3390/bios14050236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.
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Affiliation(s)
- Chunran Ma
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
- Furong Laboratory, Changsha 410082, China
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7
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Teng T, Bernal‐Chanchavac J, Stephanopoulos N, Castro CE. Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled-Coil Patches and Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307257. [PMID: 38459678 PMCID: PMC11132032 DOI: 10.1002/advs.202307257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/22/2023] [Indexed: 03/10/2024]
Abstract
DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence-specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled-coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher-order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled-coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5-10-fold increase in bending stiffness. The results provide a foundation for stimulus-responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
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Affiliation(s)
- Teng Teng
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
| | - Julio Bernal‐Chanchavac
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Nicholas Stephanopoulos
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
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8
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Jiang Q, Shang Y, Xie Y, Ding B. DNA Origami: From Molecular Folding Art to Drug Delivery Technology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2301035. [PMID: 37715333 DOI: 10.1002/adma.202301035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/08/2023] [Indexed: 09/17/2023]
Abstract
DNA molecules that store genetic information in living creatures can be repurposed as building blocks to construct artificial architectures, ranging from the nanoscale to the microscale. The precise fabrication of self-assembled DNA nanomaterials and their various applications have greatly impacted nanoscience and nanotechnology. More specifically, the DNA origami technique has realized the assembly of various nanostructures featuring rationally predesigned geometries, precise addressability, and versatile programmability, as well as remarkable biocompatibility. These features have elevated DNA origami from academic interest to an emerging class of drug delivery platform for a wide range of diseases. In this minireview, the latest advances in the burgeoning field of DNA-origami-based innovative platforms for regulating biological functions and delivering versatile drugs are presented. Challenges regarding the novel drug vehicle's safety, stability, targeting strategy, and future clinical translation are also discussed.
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Affiliation(s)
- Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
| | - Yiming Xie
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
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9
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Adžić N, Jochum C, Likos CN, Stiakakis E. Engineering Ultrasoft Interactions in Stiff All-DNA Dendrimers by Site-Specific Control of Scaffold Flexibility. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308763. [PMID: 38183376 DOI: 10.1002/smll.202308763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/10/2023] [Indexed: 01/08/2024]
Abstract
A combined experimental and theoretical study of the structural correlations in moderately concentrated suspensions of all-DNA dendrimers of the second generation (G2) with controlled scaffold rigidity is reported here. Small-angle X-ray scattering experiments in concentrated aqueous saline solutions of stiff all-DNA G2 dendritic constructs reveal a novel anomalous liquid-like phase behavior which is reflected in the calculated structure factors as a two-step increase at low scattering wave vectors. By developing a new design strategy for adjusting the particle's internal flexibility based on site-selective incorporation of single-stranded DNA linkers into the dendritic scaffold, it is shown that this unconventional type of self-organization is strongly contingent on the dendrimer's stiffness. A comprehensive computer simulation study employing dendritic models with different levels of coarse-graining, and two theoretical approaches based on effective, pair-potential interactions, remarkably confirmed the origin of this unusual liquid-like behavior. The results demonstrate that the precise control of the internal structure of the dendritic scaffold conferred by the DNA can be potentially used to engineer a rich palette of novel ultrasoft interaction potentials that could offer a route for directed self-assembly of intriguing soft matter phases and experimental realizations of a host of unusual phenomena theoretically predicted for ultrasoft interacting systems.
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Affiliation(s)
- Nataša Adžić
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, A-1090, Austria
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, Belgrade, 11080, Serbia
| | - Clemens Jochum
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10, Vienna, A-1040, Austria
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, A-1090, Austria
| | - Emmanuel Stiakakis
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425, Jülich, Germany
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10
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Duque CM, Hall DM, Tyukodi B, Hagan MF, Santangelo CD, Grason GM. Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra. Proc Natl Acad Sci U S A 2024; 121:e2315648121. [PMID: 38669182 PMCID: PMC11067059 DOI: 10.1073/pnas.2315648121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.
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Affiliation(s)
- Carlos M. Duque
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
- Department of Physics, University of Massachusetts, Amherst, MA01003
| | - Douglas M. Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
| | - Botond Tyukodi
- Department of Physics, Babes-Bolyai University, Cluj-Napoca400084, Romania
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Christian D. Santangelo
- Department of Physics, University of Massachusetts, Amherst, MA01003
- Department of Physics, Syracuse University, Syracuse, NY13210
| | - Gregory M. Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
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11
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Aqib RM, Wang Y, Liu J, Ding B. Efficient one-pot assembly of higher-order DNA nanostructures by chemically conjugated branched DNA. Chem Commun (Camb) 2024; 60:4715-4718. [PMID: 38596907 DOI: 10.1039/d4cc01097c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Chemically conjugated branched DNA was successfully synthesized by a copper-free click reaction to construct sophisticated and higher-order polyhedral DNA nanostructures with pre-defined units in one pot, which can be used as an efficient nanoplatform to precisely organize multiple gold nanoparticles in predesigned patterns.
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Affiliation(s)
- Raja Muhammad Aqib
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Woo S, Saka SK, Xuan F, Yin P. Molecular robotic agents that survey molecular landscapes for information retrieval. Nat Commun 2024; 15:3293. [PMID: 38632239 PMCID: PMC11024175 DOI: 10.1038/s41467-024-46978-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-based artificial motors have allowed the recapitulation of biological functions and the creation of new features. Here, we present a molecular robotic system that surveys molecular environments and reports spatial information in an autonomous and repeated manner. A group of molecular agents, termed 'crawlers', roam around and copy information from DNA-labeled targets, generating records that reflect their trajectories. Based on a mechanism that allows random crawling, we show that our system is capable of counting the number of subunits in example molecular complexes. Our system can also detect multivalent proximities by generating concatenated records from multiple local interactions. We demonstrate this capability by distinguishing colocalization patterns of three proteins inside fixed cells under different conditions. These mechanisms for examining molecular landscapes may serve as a basis towards creating large-scale detailed molecular interaction maps inside the cell with nanoscale resolution.
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Affiliation(s)
- Sungwook Woo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Materials Science and Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea.
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- European Molecular Biology Laboratory (EMBL), Heidelberg, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Feng Xuan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Spear Bio Inc., Woburn, MA, 01801, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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13
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Iinuma R, Chen X, Masubuchi T, Ueda T, Tadakuma H. Size-Selective Capturing of Exosomes Using DNA Tripods. J Am Chem Soc 2024; 146:10293-10298. [PMID: 38569597 PMCID: PMC11027911 DOI: 10.1021/jacs.3c11067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Fractionating and characterizing target samples are fundamental to the analysis of biomolecules. Extracellular vesicles (EVs), containing information regarding the cellular birthplace, are promising targets for biology and medicine. However, the requirement for multiple-step purification in conventional methods hinders analysis of small samples. Here, we apply a DNA origami tripod with a defined aperture of binders (e.g., antibodies against EV biomarkers), which allows us to capture the target molecule. Using exosomes as a model, we show that our tripod nanodevice can capture a specific size range of EVs with cognate biomarkers from a broad distribution of crude EV mixtures. We further demonstrate that the size of captured EVs can be controlled by changing the aperture of the tripods. This simultaneous selection with the size and biomarker approach should simplify the EV purification process and contribute to the precise analysis of target biomolecules from small samples.
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Affiliation(s)
- Ryosuke Iinuma
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- JSR
Corporation, Ibaraki, 305-0841, Japan
| | - Xiaoxia Chen
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, People’s Republic of China
| | - Takeya Masubuchi
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- Department
of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Takuya Ueda
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- Graduate
School of Science and Engineering, Waseda
University, Tokyo 162-8480, Japan
| | - Hisashi Tadakuma
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, People’s Republic of China
- Gene Editing
Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People’s Republic
of China
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14
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Aksel T, Navarro EJ, Fong N, Douglas SM. Design principles for accurate folding of DNA origami. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585609. [PMID: 38562860 PMCID: PMC10983894 DOI: 10.1101/2024.03.18.585609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate design rules, we reduced the problem of DNA strand routing to the known problem of shortest-path finding in a weighted graph. To score candidate DNA strand routes we used a thermodynamic model that accounts for enthalpic and entropic contributions of initial binding, hybridization, and DNA loop closure. We encoded and analyzed new and previously reported design heuristics. Using design principles emerging from this analysis, we redesigned and fabricated multiple shapes and compared their folding accuracy using electrophoretic mobility analysis and electron microscopy imaging. We demonstrate accurate folding can be achieved by optimizing staple routes using our model, and provide a computational framework for applying our methodology to any design.
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Affiliation(s)
- Tural Aksel
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
| | - Erik J. Navarro
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
| | - Nicholas Fong
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
| | - Shawn M. Douglas
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
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15
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Narayanan RP, Prasad A, Buchberger A, Zou L, Bernal-Chanchavac J, MacCulloch T, Fahmi NE, Yan H, Zhang F, Webber MJ, Stephanopoulos N. High-Affinity Host-Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307585. [PMID: 37849034 PMCID: PMC10922742 DOI: 10.1002/smll.202307585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Indexed: 10/19/2023]
Abstract
The combination of multiple orthogonal interactions enables hierarchical complexity in self-assembled nanoscale materials. Here, efficient supramolecular polymerization of DNA origami nanostructures is demonstrated using a multivalent display of small molecule host-guest interactions. Modification of DNA strands with cucurbit[7]uril (CB[7]) and its adamantane guest, yielding a supramolecular complex with an affinity of order 1010 m-1 , directs hierarchical assembly of origami monomers into 1D nanofibers. This affinity regime enables efficient polymerization; a lower-affinity β-cyclodextrin-adamantane complex does not promote extended structures at a similar valency. Finally, the utility of the high-affinity CB[7]-adamantane interactions is exploited to enable responsive enzymatic actuation of origami nanofibers assembled using peptide linkers. This work demonstrates the power of high-affinity CB[7]-guest recognition as an orthogonal axis to drive self-assembly in DNA nanotechnology.
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Affiliation(s)
- Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Abhay Prasad
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Lei Zou
- Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Nour Eddine Fahmi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University-Newark, Newark, NJ, 07102, USA
| | - Matthew J Webber
- Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
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16
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Evans J, Šulc P. Designing 3D multicomponent self-assembling systems with signal-passing building blocks. J Chem Phys 2024; 160:084902. [PMID: 38385517 DOI: 10.1063/5.0191282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
We introduce an allostery-mimetic building block model for the self-assembly of 3D structures. We represent the building blocks as patchy particles, where each binding site (patch) can be irreversibly activated or deactivated by binding of the particle's other controlling patches to another particle. We show that these allostery-mimetic systems can be designed to increase yields of target structures by disallowing misassembled states and can further decrease the smallest number of distinct species needed to assemble a target structure. Next, we show applications to design a programmable nanoparticle swarm for multifarious assembly: a system of particles that stores multiple possible target structures and a particular structure is recalled by presenting an external trigger signal. Finally, we outline a possible pathway for realization of such structures at nanoscale using DNA nanotechnology devices.
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Affiliation(s)
- Joshua Evans
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
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17
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Liu Y, Dai Z, Xie X, Li B, Jia S, Li Q, Li M, Fan C, Liu X. Spacer-Programmed Two-Dimensional DNA Origami Assembly. J Am Chem Soc 2024; 146:5461-5469. [PMID: 38355136 DOI: 10.1021/jacs.3c13180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Two-dimensional (2D) DNA origami assembly represents a powerful approach to the programmable design and construction of advanced 2D materials. Within the context of hybridization-mediated 2D DNA origami assembly, DNA spacers play a pivotal role as essential connectors between sticky-end regions and DNA origami units. Here, we demonstrated that programming the spacer length, which determines the binding radius of DNA origami units, could effectively tune sticky-end hybridization reactions to produce distinct 2D DNA origami arrays. Using DNA-PAINT super-resolution imaging, we unveiled the significant impact of spacer length on the hybridization efficiency of sticky ends for assembling square DNA origami (SDO) units. We also found that the assembly efficiency and pattern diversity of 2D DNA origami assemblies were critically dependent on the spacer length. Remarkably, we realized a near-unity yield of ∼98% for the assembly of SDO trimers and tetramers via this spacer-programmed strategy. At last, we revealed that spacer lengths and thermodynamic fluctuations of SDO are positively correlated, using molecular dynamics simulations. Our study thus paves the way for the precision assembly of DNA nanostructures toward higher complexity.
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Affiliation(s)
- Yongjun Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zheze Dai
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bochen Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sisi Jia
- Zhangjiang Laboratory, Shanghai 201210, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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18
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He J, Shang X, Long M, Yang C, Zhang Y, Li M, Yuan R, Xu W. Fluorescence Biosensing Based on Bifurcated DNA Scaffold-Aggregated Ag Nanocluster via Responsive Conformation Switch of Quasi-Molecular Beacon. Anal Chem 2024; 96:3480-3488. [PMID: 38351592 DOI: 10.1021/acs.analchem.3c05108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
To address the limitations of typical hairpin-structural molecular beacons, exploring the ability of a quasi-molecular beacon (qMB) to create label-free fluorescence biosensors is intriguing and remains a challenge. Herein, we propose the first example of modular qMB with the feature of a stimulation-responsive conformation switch to develop an aggregated Ag nanocluster (aAgNC) in a bifurcated DNA scaffold for fluorescently sensing a specific initiator (I*). This qMB was well designed to program four functional modules: I*-recognizable element adopting metastable stem-loop bihairpin structure and two DNA splits (exposed C3GT4 and locked C4AC4T) of aAgNC template that is separated by a tunable hairpin spacer for the customized combination of selective recognition and signaling readout. When presenting I* in an assay route, the specific hybridization induces the directional disassembly of the bihairpin unit, on which the qMB is configurationally switched to liberate the locked split. Thus, the bifurcated parent template pair of C3GT4/C4AC4T is proximal, affording in situ nucleation and clustering of emissive aAgNC. By collecting the fluorescence signal, the quantitative detection of I* is achieved. Benefiting from the ingenious programming of qMB, the recognizing and signaling integration actuates the construction of a facile and convenient fluorescent biosensor featuring rapid reaction kinetics, a wide linear range, high sensitivity, and specificity. This would provide a new paradigm to exploit versatile qMB-based biosensing platforms via stimulation-responsive conformation switches for developing various DNA-scaffolded Ag clusters.
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Affiliation(s)
- Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xin Shang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Min Long
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yuqing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Mengdie Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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19
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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20
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Wang Y, Wang H, Li Y, Yang C, Tang Y, Lu X, Fan J, Tang W, Shang Y, Yan H, Liu J, Ding B. Chemically Conjugated Branched Staples for Super-DNA Origami. J Am Chem Soc 2024; 146:4178-4186. [PMID: 38301245 DOI: 10.1021/jacs.3c13331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.
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Affiliation(s)
- Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yan Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Changping Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Yue Tang
- Arizona State University, Tempe, Arizona 85281, United States
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jing Fan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Wantao Tang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hao Yan
- Arizona State University, Tempe, Arizona 85281, United States
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Wei WS, Trubiano A, Sigl C, Paquay S, Dietz H, Hagan MF, Fraden S. Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids. Proc Natl Acad Sci U S A 2024; 121:e2312775121. [PMID: 38324570 PMCID: PMC10873614 DOI: 10.1073/pnas.2312775121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T = 3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose three-dimensional geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures.
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Affiliation(s)
- Wei-Shao Wei
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Anthony Trubiano
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Christian Sigl
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Stefan Paquay
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Hendrik Dietz
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Seth Fraden
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
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22
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Zhang Y, Chen Y, Liu X, Ling Q, Wu R, Yang J, Zhang C. Programmable Primer Switching for Regulating Enzymatic DNA Circuits. ACS NANO 2024; 18:5089-5100. [PMID: 38286819 DOI: 10.1021/acsnano.3c12000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Developing DNA strand displacement reactions (SDRs) offers crucial technical support for regulating artificial nucleic acid circuits and networks. More recently, enzymatic SDR-based DNA circuits have gained significant attention because of their modular design, high orthogonality signaling, and extremely fast reaction rates. Typical enzymatic SDRs are regulated by relatively long primers (20-30 nucleotides) that hybridize to form stable double-stranded structures, facilitating enzyme-initiated events. Implementing more flexible primer-based enzymatic SDR regulations remains challenging due to the lack of convenient and simple primer control mechanism, which consequently limits the development of enzymatic DNA circuits. In this study, we propose an approach, termed primer switching regulation, that implements programmable and flexible regulations of enzymatic circuits by introducing switchable wires into the enzymatic circuits. We applied this method to generate diverse enzymatic DNA circuits, including cascading, fan-in/fan-out, dual-rail, feed-forward, and feedback functions. Through this method, complex circuit functions can be implemented by just introducing additional switching wires without reconstructing the basic circuit frameworks. The method is experimentally demonstrated to provide flexible and programmable regulations to control enzymatic DNA circuits and has future applications in DNA computing, biosensing, and DNA storage.
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Affiliation(s)
- Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Yiming Chen
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Xuan Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Qian Ling
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
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23
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Chen Z, Xie C, Chen K, Hu Y, Xu F, Pan L. Multimode adaptive logic gates based on temperature-responsive DNA strand displacement. NANOSCALE 2024; 16:3107-3112. [PMID: 38250822 DOI: 10.1039/d3nr05980d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Living organisms switch their intrinsic biological states to survive environmental turbulence, in which temperature changes are prevalent in nature. Most artificial temperature-responsive DNA nanosystems work as switch modules that transit between "ON-OFF" states, making it difficult to construct nanosystems with diverse functions. In this study, we present a general strategy to build multimode nanosystems based on a temperature-responsive DNA strand displacement reaction. The temperature-responsive DNA strand displacement was controlled by tuning the sequence of the substrate hairpin strands and the invading strands. The nanosystems were demonstrated as logic gates that performed a set of Boolean logical functions at specific temperatures. In addition, an adaptive logic gate was fabricated that could exhibit different logic functions when placed in different temperatures. Specifically, upon the same input strands, the logic gate worked as an XOR gate at 10 °C, an OR gate at 35 °C, an AND gate at 46 °C, and was reset at 55 °C. The design and fabrication of the multifunctional nanosystems would help construct advanced temperature-responsive systems that may be used for temperature-controlled multi-stage drug delivery and thermally-controlled multi-step assembly of nanostructures.
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Affiliation(s)
- Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043, China
| | - Fei Xu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
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24
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Centola M, Poppleton E, Ray S, Centola M, Welty R, Valero J, Walter NG, Šulc P, Famulok M. A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower. NATURE NANOTECHNOLOGY 2024; 19:226-236. [PMID: 37857824 PMCID: PMC10873200 DOI: 10.1038/s41565-023-01516-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver-follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver-follower pair.
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Affiliation(s)
- Mathias Centola
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
| | - Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Max-Planck-Institute for Medical Research, Heidelberg, Germany
| | - Sujay Ray
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | | | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | - Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
- Interdisciplinary Nanoscience Center - INANO-MBG, iNANO-huset, Århus, Denmark
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA.
| | - Petr Šulc
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany.
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25
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Sun Z, Ren Y, Zhu W, Xiao Y, Wu H. DNA nanotechnology-based nucleic acid delivery systems for bioimaging and disease treatment. Analyst 2024; 149:599-613. [PMID: 38221846 DOI: 10.1039/d3an01871g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Nucleic acids, including DNA and RNA, have been considered as powerful and functional biomaterials owing to their programmable structure, good biocompatibility, and ease of synthesis. However, traditional nucleic acid-based probes have always suffered from inherent limitations, including restricted cell internalization efficiency and structural instability. In recent years, DNA nanotechnology has shown great promise for the applications of bioimaging and drug delivery. The attractive superiorities of DNA nanostructures, such as precise geometries, spatial addressability, and improved biostability, have enabled them to be a novel category of nucleic acid delivery systems for biomedical applications. In this review, we introduce the development of DNA nanotechnology, and highlight recent advances of DNA nanostructure-based delivery systems for cellular imaging and therapeutic applications. Finally, we propose the challenges as well as opportunities for the future development of DNA nanotechnology in biomedical research.
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Affiliation(s)
- Zhaorong Sun
- Department of Pharmacy, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, Shandong, 271000, China
| | - Yingjie Ren
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Wenjun Zhu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuliang Xiao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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26
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Kröll S, Niemeyer CM. Nucleic Acid-based Enzyme Cascades-Current Trends and Future Perspectives. Angew Chem Int Ed Engl 2024; 63:e202314452. [PMID: 37870888 DOI: 10.1002/anie.202314452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
The natural micro- and nanoscale organization of biomacromolecules is a remarkable principle within living cells, allowing for the control of cellular functions by compartmentalization, dimensional diffusion and substrate channeling. In order to explore these biological mechanisms and harness their potential for applications such as sensing and catalysis, molecular scaffolding has emerged as a promising approach. In the case of synthetic enzyme cascades, developments in DNA nanotechnology have produced particularly powerful scaffolds whose addressability can be programmed with nanometer precision. In this minireview, we summarize recent developments in the field of biomimetic multicatalytic cascade reactions organized on DNA nanostructures. We emphasize the impact of the underlying design principles like DNA origami, efficient strategies for enzyme immobilization, as well as the importance of experimental design parameters and theoretical modeling. We show how DNA nanostructures have enabled a better understanding of diffusion and compartmentalization effects at the nanometer length scale, and discuss the challenges and future potential for commercial applications.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
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27
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Vogt M, List J, Langecker M, Santiago I, Simmel FC, Kopperger E. Electrokinetic Torque Generation by DNA Nanorobotic Arms Studied via Single-Molecule Fluctuation Analysis. J Phys Chem B 2023; 127:10710-10722. [PMID: 38060372 DOI: 10.1021/acs.jpcb.3c05959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
DNA nanotechnology has enabled the creation of supramolecular machines, whose shape and function are inspired from traditional mechanical engineering as well as from biological examples. As DNA inherently is a highly charged biopolymer, the external application of electric fields provides a versatile, computer-programmable way to control the movement of DNA-based machines. However, the details of the electrohydrodynamic interactions underlying the electrical manipulation of these machines are complex, as the influence of their intrinsic charge, the surrounding cloud of counterions, and the effect of electrokinetic fluid flow have to be taken into account. In this work, we identify the relevant effects involved in this actuation mechanism by determining the electric response of an established DNA-based nanorobotic arm to varying design and operation parameters. Borrowing an approach from single-molecule biophysics, we determined the electrical torque exerted on the nanorobotic arms by analyzing their thermal fluctuations when oriented in an electric field. We analyze the influence of various experimental and design parameters on the "actuatability" of the nanostructures and optimize the generated torque according to these parameters. Our findings give insight into the physical processes involved in the actuation mechanism and provide general guidelines that aid in designing and efficiently operating electrically driven nanorobotic devices made from DNA.
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Affiliation(s)
- Matthias Vogt
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Jonathan List
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Martin Langecker
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Ibon Santiago
- CIC nanoGUNE BRTA, Donostia-San Sebastián 20018, Spain
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Enzo Kopperger
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
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28
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Tang W, Tong T, Wang H, Lu X, Yang C, Wu Y, Wang Y, Liu J, Ding B. A DNA Origami-Based Gene Editing System for Efficient Gene Therapy in Vivo. Angew Chem Int Ed Engl 2023; 62:e202315093. [PMID: 37906116 DOI: 10.1002/anie.202315093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
DNA nanostructures have played an important role in the development of novel drug delivery systems. Herein, we report a DNA origami-based CRISPR/Cas9 gene editing system for efficient gene therapy in vivo. In our design, a PAM-rich region precisely organized on the surface of DNA origami can easily recruit and load sgRNA/Cas9 complex by PAM-guided assembly and pre-designed DNA/RNA hybridization. After loading the sgRNA/Cas9 complex, the DNA origami can be further rolled up by the locking strands with a disulfide bond. With the incorporation of DNA aptamer and influenza hemagglutinin (HA) peptide, the cargo-loaded DNA origami can realize the targeted delivery and effective endosomal escape. After reduction by GSH, the opened DNA origami can release the sgRNA/Cas9 complex by RNase H cleavage to achieve a pronounced gene editing of a tumor-associated gene for gene therapy in vivo. This rationally developed DNA origami-based gene editing system presents a new avenue for the development of gene therapy.
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Affiliation(s)
- Wantao Tang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Ting Tong
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Changping Yang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Yushuai Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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29
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Berg WR, Berengut JF, Bai C, Wimberger L, Lee LK, Rizzuto FJ. Light-Activated Assembly of DNA Origami into Dissipative Fibrils. Angew Chem Int Ed Engl 2023; 62:e202314458. [PMID: 37903739 DOI: 10.1002/anie.202314458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.
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Affiliation(s)
- Willi R Berg
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 34-36, 14195, Berlin, Germany
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Changzhuang Bai
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Laura Wimberger
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
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30
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Zhou F, Ni H, Zhu G, Bershadsky L, Sha R, Seeman NC, Chaikin PM. Toward three-dimensional DNA industrial nanorobots. Sci Robot 2023; 8:eadf1274. [PMID: 38055806 DOI: 10.1126/scirobotics.adf1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Nanoscale industrial robots have potential as manufacturing platforms and are capable of automatically performing repetitive tasks to handle and produce nanomaterials with consistent precision and accuracy. We demonstrate a DNA industrial nanorobot that fabricates a three-dimensional (3D), optically active chiral structure from optically inactive parts. By making use of externally controlled temperature and ultraviolet (UV) light, our programmable robot, ~100 nanometers in size, grabs different parts, positions and aligns them so that they can be welded, releases the construct, and returns to its original configuration ready for its next operation. Our robot can also self-replicate its 3D structure and functions, surpassing single-step templating (restricted to two dimensions) by using folding to access the third dimension and more degrees of freedom. Our introduction of multiple-axis precise folding and positioning as a tool/technology for nanomanufacturing will open the door to more complex and useful nano- and microdevices.
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Affiliation(s)
- Feng Zhou
- Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
- Department of Physics, New York University, New York, NY, USA
- Department of Chemistry, New York University, New York, NY, USA
| | - Heng Ni
- Department of Physics, New York University, New York, NY, USA
| | - Guolong Zhu
- Department of Physics, New York University, New York, NY, USA
- Department of Chemistry, Biochemistry, and Physics, Fairleigh Dickinson University, Madison, NJ, USA
| | - Lev Bershadsky
- Department of Physics, New York University, New York, NY, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, USA
| | | | - Paul M Chaikin
- Department of Physics, New York University, New York, NY, USA
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31
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Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H. Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals. J Am Chem Soc 2023; 145:26075-26085. [PMID: 37987645 PMCID: PMC10789492 DOI: 10.1021/jacs.3c07802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven an elusive goal since its conception. Oligonucleotide frameworks provide an especially attractive route toward studying DNA-binding molecules by using three-dimensional lattices with defined sequence and structure. In this work, we site-specifically position a suite of minor groove binding molecules, and solve their structures via X-ray crystallography as a proof-of-principle toward scaffolding larger guest species. Two crystal motifs were used to precisely immobilize the molecules DAPI, Hoechst, and netropsin at defined positions in the lattice, allowing us to control occupancy within the crystal. We also solved the structure of a three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs in an antiparallel dimeric arrangement within the minor groove. Finally, we engineered a crystal designed to position both netropsin and the polyamide at two distinct locations within the same lattice. Our work elucidates the design principles for the spatial arrangement of functional guests within lattices and opens new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
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Affiliation(s)
- Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
| | - Alex Buchberger
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Skylar J W Henry
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Alexandra Novacek
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Nour Eddine Fahmi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
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32
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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33
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Jabbari A, Sameiyan E, Yaghoobi E, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Aptamer-based targeted delivery systems for cancer treatment using DNA origami and DNA nanostructures. Int J Pharm 2023; 646:123448. [PMID: 37757957 DOI: 10.1016/j.ijpharm.2023.123448] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/14/2023] [Accepted: 09/24/2023] [Indexed: 09/29/2023]
Abstract
Due to the limitations of conventional cancer treatment methods, nanomedicine has appeared as a promising alternative, allowing improved drug targeting and decreased drug toxicity. In the development of cancer nanomedicines, among various nanoparticles (NPs), DNA nanostructures are more attractive because of their precisely controllable size, shape, excellent biocompatibility, programmability, biodegradability, and facile functionalization. Aptamers are introduced as single-stranded RNA or DNA molecules with recognize their corresponding targets. So, incorporating aptamers into DNA nanostructures led to influential vehicles for bioimaging and biosensing as well as targeted cancer therapy. In this review, the recent developments in the application of aptamer-based DNA origami and DNA nanostructures in advanced cancer treatment have been highlighted. Some of the main methods of cancer treatment are classified as chemo-, gene-, photodynamic- and combined therapy. Finally, the opportunities and problems for targeted DNA aptamer-based nanocarriers for medicinal applications have also been discussed.
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Affiliation(s)
- Atena Jabbari
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elham Sameiyan
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Yaghoobi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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34
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Lee JY, Koh H, Kim DN. A computational model for structural dynamics and reconfiguration of DNA assemblies. Nat Commun 2023; 14:7079. [PMID: 37925463 PMCID: PMC10625641 DOI: 10.1038/s41467-023-42873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model successfully simulates a long-time-scale close-to-open-to-close dynamic reconfiguration of the switch structure in response to changes in ion concentration. We expect that the proposed model will offer a versatile way of designing responsive and reconfigurable DNA machines.
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Affiliation(s)
- Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Heeyuen Koh
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
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Rossi-Gendron C, El Fakih F, Bourdon L, Nakazawa K, Finkel J, Triomphe N, Chocron L, Endo M, Sugiyama H, Bellot G, Morel M, Rudiuk S, Baigl D. Isothermal self-assembly of multicomponent and evolutive DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1311-1318. [PMID: 37524905 PMCID: PMC10656289 DOI: 10.1038/s41565-023-01468-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
Thermal annealing is usually needed to direct the assembly of multiple complementary DNA strands into desired entities. We show that, with a magnesium-free buffer containing NaCl, complex cocktails of DNA strands and proteins can self-assemble isothermally, at room or physiological temperature, into user-defined nanostructures, such as DNA origamis, single-stranded tile assemblies and nanogrids. In situ, time-resolved observation reveals that this self-assembly is thermodynamically controlled, proceeds through multiple folding pathways and leads to highly reconfigurable nanostructures. It allows a given system to self-select its most stable shape in a large pool of competitive DNA strands. Strikingly, upon the appearance of a new energy minimum, DNA origamis isothermally shift from one initially stable shape to a radically different one, by massive exchange of their constitutive staple strands. This method expands the repertoire of shapes and functions attainable by isothermal self-assembly and creates a basis for adaptive nanomachines and nanostructure discovery by evolution.
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Affiliation(s)
- Caroline Rossi-Gendron
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Farah El Fakih
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Laura Bourdon
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Koyomi Nakazawa
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Julie Finkel
- Centre de Biologie Structurale, Université Montpellier, CNRS, Inserm, Montpellier, France
| | - Nicolas Triomphe
- Centre de Biologie Structurale, Université Montpellier, CNRS, Inserm, Montpellier, France
- Université Grenoble Alpes, CEA, Leti,, Grenoble, France
| | - Léa Chocron
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Masayuki Endo
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Kyoto, Japan
| | - Gaëtan Bellot
- Centre de Biologie Structurale, Université Montpellier, CNRS, Inserm, Montpellier, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France.
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36
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Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H. Site-specific arrangement and structure determination of minor groove binding molecules in self-assembled three-dimensional DNA crystals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561756. [PMID: 37873139 PMCID: PMC10592734 DOI: 10.1101/2023.10.10.561756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven elusive since its conception. Oligonucleotide frameworks provide an especially attractive route towards studying DNA-binding molecules by using three-dimensional lattices with defined sequence and structure. In this work, we site-specifically position a suite of minor groove binding molecules, and solve their structures via x-ray crystallography, as a proof-of-principle towards scaffolding larger guest species. Two crystal motifs were used to precisely immobilize the molecules DAPI, Hoechst, and netropsin at defined positions in the lattice, allowing us to control occupancy within the crystal. We also solved the structure of a three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs in an anti-parallel dimeric arrangement within the minor groove. Finally, we engineered a crystal designed to position both netropsin and the polyamide at two distinct locations within the same lattice. Our work elucidates the design principles for the spatial arrangement of functional guests within lattices and opens new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
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37
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Jahnke K, Göpfrich K. Engineering DNA-based cytoskeletons for synthetic cells. Interface Focus 2023; 13:20230028. [PMID: 37577007 PMCID: PMC10415745 DOI: 10.1098/rsfs.2023.0028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023] Open
Abstract
The development and bottom-up assembly of synthetic cells with a functional cytoskeleton sets a major milestone to understand cell mechanics and to develop man-made machines on the nano- and microscale. However, natural cytoskeletal components can be difficult to purify, deliberately engineer and reconstitute within synthetic cells which therefore limits the realization of multifaceted functions of modern cytoskeletons in synthetic cells. Here, we review recent progress in the development of synthetic cytoskeletons made from deoxyribonucleic acid (DNA) as a complementary strategy. In particular, we explore the capabilities and limitations of DNA cytoskeletons to mimic functions of natural cystoskeletons like reversible assembly, cargo transport, force generation, mechanical support and guided polymerization. With recent examples, we showcase the power of rationally designed DNA cytoskeletons for bottom-up assembled synthetic cells as fully engineerable entities. Nevertheless, the realization of dynamic instability, self-replication and genetic encoding as well as contractile force generating motors remains a fruitful challenge for the complete integration of multifunctional DNA-based cytoskeletons into synthetic cells.
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Affiliation(s)
- Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany
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38
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Teng T, Bernal-Chanchavac J, Stephanopoulos N, Castro CE. Construction and reconfiguration of dynamic DNA origami assemblies with coiled-coil patches and patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559112. [PMID: 37790447 PMCID: PMC10542533 DOI: 10.1101/2023.09.23.559112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structure and properties. Here we report the integration of DNA origami hinge nanodevices and coiled-coil peptides into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, we make multiple higher order assemblies by organizing clusters of peptides (i.e. patches) or arranging single peptides (i.e. patterns) on the surfaces of DNA origami to control the relative orientation of devices. We use coiled-coil interactions to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based actuation. Actuation of linear assemblies leads to micron scale motions and ~2.5-10-fold increase in bending stiffness. Our results provide a foundation for stimulus responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
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Affiliation(s)
- T Teng
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, United States
| | - J Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - N Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - C E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, United States
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39
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Chen K, Xie C, Chen Z, Wang S, Hu Y, Xu F, Pan L. Presketched DNA Origami Canvas for Polymerase-Driven DNA Kirigami. ACS NANO 2023; 17:17265-17272. [PMID: 37638681 DOI: 10.1021/acsnano.3c05221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Reconfigurable DNA origami provides a versatile tool to manipulate the conformation of matter on the nanometer scale. Typically, the DNA kirigami method enables the transformation of an origami structure from an initial shape to another predesigned shape by reconfiguring the staple strands. In a regular origami structure, since the perfectly matched and densely packed DNA duplexes block the removal of staple strands, the construction of finely trimmed "sub-origami" structures by the DNA kirigami method has remained challenging. Herein, we proposed a strategy to construct the presketched DNA origami canvas, where the offcut area in the canvas was sketched by loosely fixed staple strands with single-base insertion, to enhance the fineness of polymerase-driven DNA kirigami. We successfully trimmed presketched two-dimensional rectangular canvas, three-dimensional Möbius strip, and genie bottle canvases into complex letter patterns, supercoiled rings, and nanorods, respectively. Finally, we demonstrated a size-controlled DNA kirigami system: a presketched 6HB origami was trimmed into a set of shorter nanowires with predefined lengths, which quantitatively characterized the fineness of the improved DNA kirigami. The presketched origami design was a general method that applied to both 2D and 3D DNA origami structures in square and honeycomb lattices. Loosening DNA origami structures by introducing single-base insertions provides a practical approach to constructing dynamic components when designing DNA nanomachines. Furthermore, the delicate trimming of the DNA origami canvas driven by polymerase may inspire strategies for graphical information encryption and storage.
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Affiliation(s)
- Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shichen Wang
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, Hebei 050043, China
| | - Fei Xu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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40
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Lu W, Chen T, Xiao D, Qin X, Chen Y, Shi S. Application and prospects of nucleic acid nanomaterials in tumor therapy. RSC Adv 2023; 13:26288-26301. [PMID: 37670995 PMCID: PMC10476027 DOI: 10.1039/d3ra04081j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Cancer poses a great threat to human life, and current cancer treatments, such as radiotherapy, chemotherapy, and surgery, have significant side effects and limitations that hinder their application. Nucleic acid nanomaterials have specific spatial configurations and can be used as nanocarriers to deliver different therapeutic drugs, thereby enabling various biomedical applications, such as biosensors and cancer therapy. In recent decades, a variety of DNA nanostructures have been synthesized, and they have demonstrated remarkable potential in cancer therapy related applications, such as DNA origami structures, tetrahedral framework nucleic acids, and dynamic DNA nanostructures. Importantly, more attention is also being paid to RNA nanostructures, which play an important role in gene therapy. Therefore, this review introduces the developmental history of nucleic acid nanotechnology, summarizes the applications of DNA and RNA nanostructures for tumor treatment, and discusses the development opportunities for nucleic acid nanomaterials in the future.
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Affiliation(s)
- Weitong Lu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu 610041 Sichuan China
| | - Tianyu Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu 610041 Sichuan China
| | - Dexuan Xiao
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu 610041 Sichuan China
| | - Xin Qin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu 610041 Sichuan China
| | - Yang Chen
- Department of Pediatric Surgery, Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University Chengdu Sichuan 610041 China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu 610041 Sichuan China
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41
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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42
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Alexander S, Moghadam MG, Rothenbroker M, Y T Chou L. Addressing the in vivo delivery of nucleic-acid nanostructure therapeutics. Adv Drug Deliv Rev 2023; 199:114898. [PMID: 37230305 DOI: 10.1016/j.addr.2023.114898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
DNA and RNA nanostructures are being investigated as therapeutics, vaccines, and drug delivery systems. These nanostructures can be functionalized with guests ranging from small molecules to proteins with precise spatial and stoichiometric control. This has enabled new strategies to manipulate drug activity and to engineer devices with novel therapeutic functionalities. Although existing studies have offered encouraging in vitro or pre-clinical proof-of-concepts, establishing mechanisms of in vivo delivery is the new frontier for nucleic-acid nanotechnologies. In this review, we first provide a summary of existing literature on the in vivo uses of DNA and RNA nanostructures. Based on their application areas, we discuss current models of nanoparticle delivery, and thereby highlight knowledge gaps on the in vivo interactions of nucleic-acid nanostructures. Finally, we describe techniques and strategies for investigating and engineering these interactions. Together, we propose a framework to establish in vivo design principles and advance the in vivo translation of nucleic-acid nanotechnologies.
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Affiliation(s)
- Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | | | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
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43
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Yang S, Wang Y, Wang Q, Li F, Ling D. DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:340-355. [PMID: 37501793 PMCID: PMC10369495 DOI: 10.1021/cbmi.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/07/2023] [Indexed: 07/29/2023]
Abstract
DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.
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Affiliation(s)
- Shengfei Yang
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuqi Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Qiyue Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Fangyuan Li
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
| | - Daishun Ling
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
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44
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Dai L, Hu X, Ji M, Ma N, Xing H, Zhu JJ, Min Q, Tian Y. Programming the morphology of DNA origami crystals by magnesium ion strength. Proc Natl Acad Sci U S A 2023; 120:e2302142120. [PMID: 37399399 PMCID: PMC10334761 DOI: 10.1073/pnas.2302142120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/31/2023] [Indexed: 07/05/2023] Open
Abstract
Harnessing the programmable nature of DNA origami for controlling structural features in crystalline materials affords opportunities to bring crystal engineering to a remarkable level. However, the challenge of crystallizing a single type of DNA origami unit into varied structural outcomes remains, given the requirement for specific DNA designs for each targeted structure. Here, we show that crystals with distinct equilibrium phases and shapes can be realized using a single DNA origami morphology with an allosteric factor to modulate the binding coordination. As a result, origami crystals undergo phase transitions from a simple cubic lattice to a simple hexagonal (SH) lattice and eventually to a face-centered cubic (FCC) lattice. After selectively removing internal nanoparticles from DNA origami building blocks, the body-centered tetragonal and chalcopyrite lattice are derived from the SH and FCC lattices, respectively, revealing another phase transition involving crystal system conversions. The rich phase space was realized through the de novo synthesis of crystals under varying solution environments, followed by the individual characterizations of the resulting products. Such phase transitions can lead to associated transitions in the shape of the resulting products. Hexagonal prism crystals, crystals characterized by triangular facets, and twinned crystals are observed to form from SH and FCC systems, which have not previously been experimentally realized by DNA origami crystallization. These findings open a promising pathway toward accessing a rich phase space with a single type of building block and wielding other instructions as tools to develop crystalline materials with tunable properties.
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Affiliation(s)
- Lizhi Dai
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Xiaoxue Hu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Min Ji
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Ningning Ma
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Jun-Jie Zhu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Qianhao Min
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
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45
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Kim M, Lee C, Jeon K, Lee JY, Kim YJ, Lee JG, Kim H, Cho M, Kim DN. Harnessing a paper-folding mechanism for reconfigurable DNA origami. Nature 2023; 619:78-86. [PMID: 37407684 DOI: 10.1038/s41586-023-06181-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/09/2023] [Indexed: 07/07/2023]
Abstract
The paper-folding mechanism has been widely adopted in building of reconfigurable macroscale systems because of its unique capabilities and advantages in programming variable shapes and stiffness into a structure1-5. However, it has barely been exploited in the construction of molecular-level systems owing to the lack of a suitable design principle, even though various dynamic structures based on DNA self-assembly6-9 have been developed10-23. Here we propose a method to harness the paper-folding mechanism to create reconfigurable DNA origami structures. The main idea is to build a reference, planar wireframe structure24 whose edges follow a crease pattern in paper folding so that it can be folded into various target shapes. We realized several paper-like folding and unfolding patterns using DNA strand displacement25 with high yield. Orthogonal folding, repeatable folding and unfolding, folding-based microRNA detection and fluorescence signal control were demonstrated. Stimuli-responsive folding and unfolding triggered by pH or light-source change were also possible. Moreover, by employing hierarchical assembly26 we could expand the design space and complexity of the paper-folding mechanism in a highly programmable manner. Because of its high programmability and scalability, we expect that the proposed paper-folding-based reconfiguration method will advance the development of complex molecular systems.
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Affiliation(s)
- Myoungseok Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Kyounghwa Jeon
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Young-Joo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Jae Gyung Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Hyunsu Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Maenghyo Cho
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea.
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea.
- Institute of Engineering Research, Seoul National University, Seoul, Korea.
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46
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Ahmad K, Javed A, Lanphere C, Coveney PV, Orlova EV, Howorka S. Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun 2023; 14:3630. [PMID: 37336895 DOI: 10.1038/s41467-023-38681-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/11/2023] [Indexed: 06/21/2023] Open
Abstract
DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, both in simple solvents as well as more complex and diverse anisotropic environments. Here we analyse an archetypal six-duplex DNA nanoarchitecture with single-particle cryo-electron microscopy and molecular dynamics simulations in solvents of tunable ionic strength and within the anisotropic environment of biological membranes. Outside lipid bilayers, the six-duplex bundle lacks the designed symmetrical barrel-type architecture. Rather, duplexes are arranged in non-hexagonal fashion and are disorted to form a wider, less elongated structure. Insertion into lipid membranes, however, restores the anticipated barrel shape due to lateral duplex compression by the bilayer. The salt concentration has a drastic impact on the stability of the inserted barrel-shaped DNA nanopore given the tunable electrostatic repulsion between the negatively charged duplexes. By synergistically combining experiments and simulations, we increase fundamental understanding into the environment-dependent structural dynamics of a widely used nanoarchitecture. This insight will pave the way for future engineering and biosensing applications.
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Affiliation(s)
- Katya Ahmad
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK
| | - Abid Javed
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Conor Lanphere
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK
| | - Peter V Coveney
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK.
- Advanced Research Computing Centre, University College London, London, WC1H 0AJ, UK.
- Informatics Institute, University of Amsterdam, Amsterdam, 1090 GH, The Netherlands.
| | - Elena V Orlova
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK.
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK.
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Abstract
DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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48
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Watanabe K, Kawamata I, Murata S, Suzuki Y. Multi-Reconfigurable DNA Origami Nanolattice Driven by the Combination of Orthogonal Signals. JACS AU 2023; 3:1435-1442. [PMID: 37234113 PMCID: PMC10206592 DOI: 10.1021/jacsau.3c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/01/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
The progress of the scaffolded DNA origami technology has enabled the construction of various dynamic nanodevices imitating the shapes and motions of mechanical elements. To further expand the achievable configurational changes, the incorporation of multiple movable joints into a single DNA origami structure and their precise control are desired. Here, we propose a multi-reconfigurable 3 × 3 lattice structure consisting of nine frames with rigid four-helix struts connected with flexible 10-nucleotide joints. The configuration of each frame is determined by the arbitrarily selected orthogonal pair of signal DNAs, resulting in the transformation of the lattice into various shapes. We also demonstrated sequential reconfiguration of the nanolattice and its assemblies from one into another via an isothermal strand displacement reaction at physiological temperatures. Our modular and scalable design approach could serve as a versatile platform for a variety of applications that require reversible and continuous shape control with nanoscale precision.
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Affiliation(s)
- Kotaro Watanabe
- Department
of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Ibuki Kawamata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Satoshi Murata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Yuki Suzuki
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8578, Japan
- Department
of Chemistry for Materials, Graduate School of Engineering, Mie University, 1577 Kurimamachiya-Cho, Tsu 514-8507, Mie, Japan
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49
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He Z, Shi K, Li J, Chao J. Self-assembly of DNA origami for nanofabrication, biosensing, drug delivery, and computational storage. iScience 2023; 26:106638. [PMID: 37187699 PMCID: PMC10176269 DOI: 10.1016/j.isci.2023.106638] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Since the pioneering work of immobile DNA Holliday junction by Ned Seeman in the early 1980s, the past few decades have witnessed the development of DNA nanotechnology. In particular, DNA origami has pushed the field of DNA nanotechnology to a new level. It obeys the strict Watson-Crick base pairing principle to create intricate structures with nanoscale accuracy, which greatly enriches the complexity, dimension, and functionality of DNA nanostructures. Benefiting from its high programmability and addressability, DNA origami has emerged as versatile nanomachines for transportation, sensing, and computing. This review will briefly summarize the recent progress of DNA origami, two-dimensional pattern, and three-dimensional assembly based on DNA origami, followed by introduction of its application in nanofabrication, biosensing, drug delivery, and computational storage. The prospects and challenges of assembly and application of DNA origami are also discussed.
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Affiliation(s)
- Zhimei He
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Kejun Shi
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jinggang Li
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Corresponding author
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50
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Wang Y, Sensale S, Pedrozo M, Huang CM, Poirier MG, Arya G, Castro CE. Steric Communication between Dynamic Components on DNA Nanodevices. ACS NANO 2023; 17:8271-8280. [PMID: 37072126 PMCID: PMC10173695 DOI: 10.1021/acsnano.2c12455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex geometry, programmed motion, rapid actuation, force application, and various kinds of sensing modalities. Advanced robotic functions like feedback control, autonomy, or programmed routines also require the ability to transmit signals among subcomponents. Prior work in DNA nanotechnology has established approaches for signal transmission, for example through diffusing strands or structurally coupled motions. However, soluble communication is often slow and structural coupling of motions can limit the function of individual components, for example to respond to the environment. Here, we introduce an approach inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. These components undergo separate thermal fluctuations where certain conformations of one arm will sterically occlude conformations of the distal arm. We implement this approach in a DNA origami device consisting of two stiff arms each connected to a base platform via a flexible hinge joint. We demonstrate the ability for one arm to sterically regulate both the range of motion and the conformational state (latched or freely fluctuating) of the distal arm, results that are quantitatively captured by mesoscopic simulations using experimentally informed energy landscapes for hinge-angle fluctuations. We further demonstrate the ability to modulate signal transmission by mechanically tuning the range of thermal fluctuations and controlling the conformational states of the arms. Our results establish a communication mechanism well-suited to transmit signals between thermally fluctuating dynamic components and provide a path to transmitting signals where the input is a dynamic response to parameters like force or solution conditions.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sebastian Sensale
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Miguel Pedrozo
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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