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Hasanzadeh A, Ebadati A, Saeedi S, Kamali B, Noori H, Jamei B, Hamblin MR, Liu Y, Karimi M. Nucleic acid-responsive smart systems for controlled cargo delivery. Biotechnol Adv 2024; 74:108393. [PMID: 38825215 DOI: 10.1016/j.biotechadv.2024.108393] [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: 08/21/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arefeh Ebadati
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kamali
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Jamei
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
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2
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Kanehira Y, Kogikoski S, Titov E, Tapio K, Mostafa A, Bald I. Watching a Single Enzyme at Work Using Single-Molecule Surface-Enhanced Raman Scattering and DNA Origami-Based Plasmonic Antennas. ACS NANO 2024. [PMID: 39074854 DOI: 10.1021/acsnano.4c03384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The detection of a single-enzyme catalytic reaction by surfaced-enhanced Raman scattering (SERS) is presented by utilizing DNA origami-based plasmonic antennas. A single horseradish peroxidase (HRP) was accommodated on a DNA origami nanofork plasmonic antenna (DONA) containing gold nanoparticles, enabling the tracing of single-molecule SERS signals during the peroxide reduction reaction. This allows monitoring of the structure of a single enzymatic catalytic center and products under suitable liquid conditions. Herein, we demonstrate the chemical changes of HRP and the appearance of tetramethylbenzidine (TMB), which works as a hydrogen donor before and after the catalytic reaction. The results show that the iron in HRP adopts Fe4+ and low spin states with the introduction of H2O2, indicating compound-I formation. Density functional theory (DFT) calculations were performed for later catalytic steps to rationalize the experimental Raman/SERS spectra. The presented data provide several possibilities for tracking single biomolecules in situ during a chemical reaction and further developing plasmon-enhanced biocatalysis.
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Affiliation(s)
- Yuya Kanehira
- Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Sergio Kogikoski
- Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Evgenii Titov
- Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Kosti Tapio
- Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Amr Mostafa
- Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
- Dynamics of Molecules and Clusters Department, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, 18223 Prague, Czech Republic
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3
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Bienau A, Jäkel AC, Simmel FC. Cell-Free Gene Expression in Bioprinted Fluidic Networks. ACS Synth Biol 2024. [PMID: 39042670 DOI: 10.1021/acssynbio.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
The realization of soft robotic devices with life-like properties requires the engineering of smart, active materials that can respond to environmental cues in similar ways as living cells or organisms. Cell-free expression systems provide an approach for embedding dynamic molecular control into such materials that avoids many of the complexities associated with genuinely living systems. Here, we present a strategy to integrate cell-free protein synthesis within agarose-based hydrogels that can be spatially organized and supplied by a synthetic vasculature. We first utilize an indirect printing approach with a commercial bioprinter and Pluronic F-127 as a fugitive ink to define fluidic channel structures within the hydrogels. We then investigate the impact of the gel matrix on the expression of proteins in E. coli cell-extract, which is found to depend on the gel density and the dilution of the expression system. When supplying the vascularized hydrogels with reactants, larger components such as DNA plasmids are confined to the channels or immobilized in the gels while nanoscale reaction components can diffusively spread within the gel. Using a single supply channel, we demonstrate different spatial protein concentration profiles emerging from different cell-free gene circuits comprising production, gene activation, and negative feedback. Variation of the channel design allows the creation of specific concentration profiles such as a long-term stable gradient or the homogeneous supply of a hydrogel with proteins.
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Affiliation(s)
- Alexandra Bienau
- TU Munich, School of Natural Sciences, Department of Bioscience, 85748 Garching b. München, Germany
| | - Anna C Jäkel
- TU Munich, School of Natural Sciences, Department of Bioscience, 85748 Garching b. München, Germany
| | - Friedrich C Simmel
- TU Munich, School of Natural Sciences, Department of Bioscience, 85748 Garching b. München, Germany
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4
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Sharma A, Vaswani P, Bhatia D. Revolutionizing cancer therapy using tetrahedral DNA nanostructures as intelligent drug delivery systems. NANOSCALE ADVANCES 2024; 6:3714-3732. [PMID: 39050960 PMCID: PMC11265600 DOI: 10.1039/d4na00145a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/24/2024] [Indexed: 07/27/2024]
Abstract
DNA nanostructures have surfaced as intriguing entities with vast potential in biomedicine, notably in the drug delivery area. Tetrahedral DNA nanostructures (TDNs) have received worldwide attention from among an array of different DNA nanostructures due to their extraordinary stability, great biocompatibility, and ease of functionalization. TDNs could be readily synthesized, making them attractive carriers for chemotherapeutic medicines, nucleic acid therapeutics, and imaging probes. Their varied uses encompass medication delivery, molecular diagnostics, biological imaging, and theranostics. This review extensively highlights the mechanisms of functional modification of TDNs and their applications in cancer therapy. Additionally, it discusses critical concerns and unanswered problems that require attention to increase the future application of TDNs in developing cancer treatment.
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Affiliation(s)
- Ayushi Sharma
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University Mathura Uttar Pradesh-281406 India
| | - Payal Vaswani
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj 382355 Gandhinagar India
| | - Dhiraj Bhatia
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj 382355 Gandhinagar India
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5
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Xu J, Deng H, Wu L, Song J, Feng X, Liu Y, Wang GA, Li F. Binder-Responsive DNA Strand Displacement Enables High-Throughput and High-Fidelity Discovering of Small Molecular DNA Binders. Anal Chem 2024. [PMID: 39016332 DOI: 10.1021/acs.analchem.4c02520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
High-throughput screening (HTS) is pivotal in the discovery of small molecules that bind to DNA, yet there are limited sensing mechanisms available for designing HTS assays for DNA binders. Herein, we introduce a binder-responsive toehold-mediated DNA strand displacement (BR-TMSD) technique featuring programmable reaction kinetics in response to DNA-binder interactions. When two DNA binders are used, BR-TMSD is initiated through a rapid binder displacement, followed by the DNA strand displacement. The orthogonal displacement reactions of BR-TMSD enables a high-fidelity, dual-channel HTS assay, returning 19 new DNA binders from a library of 1,170 compounds.
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Affiliation(s)
- Junpeng Xu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Hui Deng
- Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lang Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Junfeng Song
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yuhe Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China
- School of Biological Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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6
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Peter ME, Bastings MMC. Unfolding a death signal to treat rheumatoid arthritis. NATURE MATERIALS 2024; 23:882-883. [PMID: 38956351 DOI: 10.1038/s41563-024-01936-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Affiliation(s)
- Marcus E Peter
- Department of Medicine, Division of Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Maartje M C Bastings
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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7
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Ji W, Xiong X, Cao M, Zhu Y, Li L, Wang F, Fan C, Pei H. Encoding signal propagation on topology-programmed DNA origami. Nat Chem 2024:10.1038/s41557-024-01565-2. [PMID: 38886615 DOI: 10.1038/s41557-024-01565-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/24/2024] [Indexed: 06/20/2024]
Abstract
Biological systems often rely on topological transformation to reconfigure connectivity between nodes to guide the flux of molecular information. Here we develop a topology-programmed DNA origami system that encodes signal propagation at the nanoscale, analogous to topologically efficient information processing in cellular systems. We present a systematic molecular implementation of topological operations involving 'glue-cut' processes that can prompt global conformational change of DNA origami structures, with demonstrated major topological properties including genus, number of boundary components and orientability. By spatially arranging reactive DNA hairpins, we demonstrate signal propagation across transmission paths of varying lengths and orientations, and curvatures on the curved surfaces of three-dimensional origamis. These DNA origamis can also form dynamic scaffolds for regulating the spatial and temporal signal propagations whereby topological transformations spontaneously alter the location of nodes and boundary of signal propagation network. We anticipate that our strategy for topological operations will provide a general route to manufacture dynamic DNA origami nanostructures capable of performing global structural transformations under programmable control.
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Affiliation(s)
- Wei Ji
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xiewei Xiong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Mengyao Cao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Yun Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Fei Wang
- 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, 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, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
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8
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Wu H, Zhang T, Qin Y, Xia X, Bai T, Gu H, Wei B. Expanding DNA Origami Design Freedom with De Novo Synthesized Scaffolds. J Am Chem Soc 2024; 146:16076-16084. [PMID: 38803270 DOI: 10.1021/jacs.4c03148] [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: 05/29/2024]
Abstract
The construction of DNA origami nanostructures is heavily dependent on the folding of the scaffold strand, which is typically a single-stranded DNA genome extracted from a bacteriophage (M13). Custom scaffolds can be prepared in a number of methods, but they are not widely accessible to a broad user base in the DNA nanotechnology community. Here, we explored new design and construction possibilities with custom scaffolds prepared in our cost- and time-efficient production pipeline. According to the pipeline, we de novo produced a variety of scaffolds of specified local and global sequence characteristics and consequent origami constructs of modular arrangement in morphologies and functionalities. Taking advantage of this strategy of template-free scaffold production, we also designed and produced three-letter-coded scaffolds that can fold into designated morphologies rapidly at room temperature. The expanded design and construction freedom immediately brings in many new research opportunities and invites many more on the horizon.
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Affiliation(s)
- Hongrui Wu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tianqing Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yan Qin
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xinwei Xia
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 201108 ,China
| | - Tanxi Bai
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Hongzhou Gu
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 201108 ,China
| | - Bryan Wei
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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9
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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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10
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Huster D, Maiti S, Herrmann A. Phospholipid Membranes as Chemically and Functionally Tunable Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312898. [PMID: 38456771 DOI: 10.1002/adma.202312898] [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: 11/29/2023] [Revised: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107, Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Andreas Herrmann
- Freie Universität Berlin, Department Chemistry and Biochemistry, SupraFAB, Altensteinstr. 23a, D-14195, Berlin, Germany
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11
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Reinsalu O, Ernits M, Linko V. Liposome-based hybrid drug delivery systems with DNA nanostructures and metallic nanoparticles. Expert Opin Drug Deliv 2024; 21:905-920. [PMID: 38962823 DOI: 10.1080/17425247.2024.2375389] [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: 03/28/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024]
Abstract
INTRODUCTION This review discusses novel hybrid assemblies that are based on liposomal formulations. The focus is on the hybrid constructs that are formed through the integration of liposomes/vesicles with other nano-objects such as nucleic acid nanostructures and metallic nanoparticles. The aim is to introduce some of the recent, specific examples that bridge different technologies and thus may form a new platform for advanced drug delivery applications. AREAS COVERED We present selected examples of liposomal formulations combined with complex nanostructures either based on biomolecules like DNA origami or on metallic materials - metal/metal oxide/magnetic particles and metallic nanostructures, such as metal organic frameworks - together with their applications in drug delivery and beyond. EXPERT OPINION Merging the above-mentioned techniques could lead to development of drug delivery vehicles with the most desirable properties; multifunctionality, biocompatibility, high drug loading efficiency/accuracy/capacity, and stimuli-responsiveness. In the near future, we believe that especially the strategies combining dynamic, triggerable and programmable DNA nanostructures and liposomes could be used to create artificial liposome clusters for multiple applications such as examining protein-mediated interactions between lipid bilayers and channeling materials between liposomes for enhanced pharmacokinetic properties in drug delivery.
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Affiliation(s)
- Olavi Reinsalu
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Ernits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Veikko Linko
- Institute of Technology, University of Tartu, Tartu, Estonia
- Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, Espoo, Finland
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12
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Yang L, Tang Q, Zhang M, Tian Y, Chen X, Xu R, Ma Q, Guo P, Zhang C, Han D. A spatially localized DNA linear classifier for cancer diagnosis. Nat Commun 2024; 15:4583. [PMID: 38811607 PMCID: PMC11136972 DOI: 10.1038/s41467-024-48869-y] [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: 09/09/2023] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
Molecular computing is an emerging paradigm that plays an essential role in data storage, bio-computation, and clinical diagnosis with the future trends of more efficient computing scheme, higher modularity with scaled-up circuity and stronger tolerance of corrupted inputs in a complex environment. Towards these goals, we construct a spatially localized, DNA integrated circuits-based classifier (DNA IC-CLA) that can perform neuromorphic architecture-based computation at a molecular level for medical diagnosis. The DNA-based classifier employs a two-dimensional DNA origami as the framework and localized processing modules as the in-frame computing core to execute arithmetic operations (e.g. multiplication, addition, subtraction) for efficient linear classification of complex patterns of miRNA inputs. We demonstrate that the DNA IC-CLA enables accurate cancer diagnosis in a faster (about 3 h) and more effective manner in synthetic and clinical samples compared to those of the traditional freely diffusible DNA circuits. We believe that this all-in-one DNA-based classifier can exhibit more applications in biocomputing in cells and medical diagnostics.
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Affiliation(s)
- Linlin Yang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, 264003, Yantai, China
| | - Qian Tang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Mingzhi Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Yuan Tian
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xiaoxing Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Rui Xu
- Intellinosis Biotech Co.Ltd., 201112, Shanghai, China
| | - Qian Ma
- Intellinosis Biotech Co.Ltd., 201112, Shanghai, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
- Intellinosis Biotech Co.Ltd., 201112, Shanghai, China.
| | - Da Han
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
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13
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Silva-Santos AR, Sousa Rosa S, Marques MPC, Azevedo AM, Prazeres DMF. Quantification of ssDNA Scaffold Production by Ion-Pair Reverse Phase Chromatography. ACS OMEGA 2024; 9:22619-22624. [PMID: 38826531 PMCID: PMC11137683 DOI: 10.1021/acsomega.3c10533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 06/04/2024]
Abstract
DNA origami is an emerging technology that can be used as a nanoscale platform in numerous applications ranging from drug delivery systems to biosensors. The DNA nanostructures are assembled from large single-stranded DNA (ssDNA) scaffolds, ranging from hundreds to thousands of nucleotides and from short staple strands. Scaffolds are usually obtained by asymmetric PCR (aPCR) or Escherichia coli infection/transformation with phages or phagemids. Scaffold quantification is typically based on agarose gel electrophoresis densitometry for molecules obtained by aPCR, or by UV absorbance, in the case of scaffolds obtained by infection or transformation. Although these methods are well-established and easy-to-apply, the results obtained are often inaccurate due to the lack of selectivity and sensitivity in the presence of impurities. Herein, we present an HPLC method based on ion-pair reversed-phase (IP-RP) chromatography to quantify DNA scaffolds. Using IP-RP chromatography, ssDNA products (449 and 1000 nt) prepared by aPCR were separated from impurities and from the double stranded (ds) DNA byproduct. Additionally, both ss and dsDNA were quantified with high accuracy. The method was used to guide the optimization of the production of ssDNA by aPCR, which targeted the maximization of the ratio of ssDNA to dsDNA obtained. Moreover, ssDNA produced from phage infection of E. coli cells was also quantified by IP-RP using commercial ssDNA from the M13mp18 phage as a standard.
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Affiliation(s)
- A. Rita Silva-Santos
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sara Sousa Rosa
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Marco P. C. Marques
- Department
of Biochemical Engineering, University College
London, Bernard Katz Building, Gordon Street, London WC1H 0AH, U.K.
| | - Ana M. Azevedo
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Duarte Miguel F. Prazeres
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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14
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Aqib RM, Umer A, Li J, Liu J, Ding B. Light Responsive DNA Nanomaterials and Their Biomedical Applications. Chem Asian J 2024; 19:e202400226. [PMID: 38514391 DOI: 10.1002/asia.202400226] [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: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
DNA nanomaterials have been widely employed for various biomedical applications. With rapid development of chemical modification of nucleic acid, serials of stimuli-responsive elements are included in the multifunctional DNA nanomaterials. In this review, we summarize the recent advances in light responsive DNA nanomaterials based on photocleavage/photodecage, photoisomerization, and photocrosslinking for efficient bioimaging (including imaging of small molecule, microRNA, and protein) and drug delivery (including delivery of small molecule, nucleic acid, and gene editing system). We also discuss the remaining challenges and future perspectives of the light responsive DNA nanomaterials in biomedical applications.
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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
| | - Arsalan Umer
- 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
| | - Jialin Li
- 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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15
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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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16
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Shapiro A, Joseph N, Mellul N, Abu-Horowitz A, Mizrahi B, Bachelet I. Folding molecular origami from ribosomal RNA. J Nanobiotechnology 2024; 22:218. [PMID: 38698435 PMCID: PMC11067225 DOI: 10.1186/s12951-024-02489-2] [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: 07/18/2023] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Approximately 80 percent of the total RNA in cells is ribosomal RNA (rRNA), making it an abundant and inexpensive natural source of long, single-stranded nucleic acid, which could be used as raw material for the fabrication of molecular origami. In this study, we demonstrate efficient and robust construction of 2D and 3D origami nanostructures utilizing cellular rRNA as a scaffold and DNA oligonucleotide staples. We present calibrated protocols for the robust folding of contiguous shapes from one or two rRNA subunits that are efficient to allow folding using crude extracts of total RNA. We also show that RNA maintains stability within the folded structure. Lastly, we present a novel and comprehensive analysis and insights into the stability of RNA:DNA origami nanostructures and demonstrate their enhanced stability when coated with polylysine-polyethylene glycol in different temperatures, low Mg2+ concentrations, human serum, and in the presence of nucleases (DNase I or RNase H). Thus, laying the foundation for their potential implementation in emerging biomedical applications, where folding rRNA into stable structures outside and inside cells would be desired.
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Affiliation(s)
- Anastasia Shapiro
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel
- Technion, Faculty of Biotechnology and Food Engineering, 32000, Haifa, Israel
| | - Noah Joseph
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel
| | - Nadav Mellul
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel
| | | | - Boaz Mizrahi
- Technion, Faculty of Biotechnology and Food Engineering, 32000, Haifa, Israel
| | - Ido Bachelet
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel.
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17
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Ketkar RN, Dey P, Sodnawar T, Sharma S, M M, Dutta Choudhury S, Sadhukhan N. Dual Functional Microcapsule based on Monodisperse Short PEG Amphiphile for Drug Encapsulation and Protein Affinity Controlled Release. Chem Asian J 2024; 19:e202400144. [PMID: 38487959 DOI: 10.1002/asia.202400144] [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: 02/08/2024] [Revised: 03/09/2024] [Indexed: 04/12/2024]
Abstract
A short monodisperse poly(ethylene glycol) (PEG) and a neutral organic rotamer conjugate TEG-BTA-2 amphiphile was designed for the construction of a stimuli-responsive switchable self-assembled structure for drug encapsulation by noncovalent interaction and targeted controlled delivery. A short PEG, tetraethylene glycol (TEG) was covalently attached with a neutral organic rotamer benzothiazole dye (BTA-2) affording the neutral TEG-BTA-2 (<500 D). The TEG-BTA-2 is self-assembled into a microsphere in an aqueous medium, but remarkably undergoes morphology change switching to a rice-like microcapsule for curcumin encapsulation. Curcumin-loaded microcapsules were stable in an aqueous solution, however, were noticed disintegrating upon the addition of BSA protein. This is possibly due to an interaction with BSA protein leading to a protein affinity-controlled curcumin release in a neutral PBS buffer. Moreover, cell internalization of the neutral amphiphile TEG-BTA-2 into A549 cells was observed by fluorescence microscopy, providing an opportunity for application as a molecular vehicle for targeted drug delivery and monitoring.
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Affiliation(s)
- Rohit N Ketkar
- Department of Speciality Chemicals Technology, Institute of Chemical Technology, Matunga (E), Mumbai, Maharashtra, 400019, India
| | - Paritosh Dey
- Department of Speciality Chemicals Technology, Institute of Chemical Technology, Matunga (E), Mumbai, Maharashtra, 400019, India
| | - Triveni Sodnawar
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkind Road, Pune, Maharashtra, 411007, India
| | - Shilpy Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkind Road, Pune, Maharashtra, 411007, India
| | - Manikandan M
- Medicinal Chemistry and Cell Biology Laboratory, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, Maharashtra, 400005, India
| | - Sharmistha Dutta Choudhury
- Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute Anushaktinagar, Mumbai, 400094, India
| | - Nabanita Sadhukhan
- Department of Speciality Chemicals Technology, Institute of Chemical Technology, Matunga (E), Mumbai, Maharashtra, 400019, India
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18
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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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19
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Alexander S, Wang WX, Tseng CY, Douglas TR, Chou LYT. High-Throughput, Label-Free Detection of DNA Origami in Single-Cell Suspensions Using origamiFISH-Flow. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400236. [PMID: 38686679 DOI: 10.1002/smll.202400236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/28/2024] [Indexed: 05/02/2024]
Abstract
Structural DNA nanotechnology enables custom fabrication of nanoscale devices and promises diverse biological applications. However, the effects of design on DNA nanostructure (DN)-cell interactions in vitro and in vivo are not yet well-characterized. origamiFISH is a recently developed technique for imaging DNs in cells and tissues. Compared to the use of fluorescent tags, origamiFISH offers label-free and structure-agnostic detection of DNs with significantly improved sensitivity. Here, the origamiFISH technique is extended to quantify DNs in single-cell suspensions, including in nonadherent cells such as subsets of immune cells, via readout by flow cytometry. This method, referred to as origamiFISH-Flow, is high-throughput (e.g., 10 000 cells per second) and compatible with immunostaining for concurrent cell-type and cell-state characterization. It is shown that origamiFISH-Flow provides 20-fold higher signal-to-noise ratio for DN detection compared to dye labeling approaches, leading to the capture of >25-fold more DN+ cells under single-picomolar DN uptake concentrations. Additionally, the use of origamiFISH-Flow is validated to profile the uptake of various DN shapes across multiple cell lines and splenocytes, as well as to quantify in vivo DN accumulation in lymphoid organs. Together, origamiFISH-Flow offers a new tool to interrogate DN interactions with cells and tissues, while providing insights for tailoring their designs in bio-applications.
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Affiliation(s)
- Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Chung-Yi Tseng
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Travis R Douglas
- 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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20
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Zhang X, Liu X, Zhang X, Cui S, Yao Y, Wang B, Zhang Q. Arbitrary Digital DNA Computing: A Programmable Molecular Perceptron Driven by Lambda Exonuclease for Lighting up Concatenated Circuits. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38688864 DOI: 10.1021/acsami.4c03486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
DNA circuits, as a type of biochemical system, have the capability to synchronize the perception of molecular information with a chemical reaction response and directly process the molecular characteristic information in biological activities, making them a crucial area in molecular digital computing and smart bioanalytical applications. Instead of cascading logic gates, the traditional research approach achieves multiple logic operations which limits the scalability of DNA circuits and increases the development costs. Based on the interface reaction mechanism of Lambda exonuclease, the molecular perceptron proposed in this study, with the need for only adjusting weight and bias parameters to alter the corresponding logic expressions, enhances the versatility of the molecular circuits. We also establish a mathematical model and an improved heuristic algorithm for solving weights and bias parameters for arbitrary logic operations. The simulation and FRET experiment results of a series of logic operations demonstrate the universality of molecular perceptron. We hope the proposed molecular perceptron can introduce a new design paradigm for molecular circuits, fostering innovation and development in biomedical research related to biosensing, targeted therapy, and nanomachines.
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Affiliation(s)
- Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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21
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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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22
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Zhao H, Yi D, Li L, Zhao Y, Li M. Modular Weaving DNAzyme in Skeleton of DNA Nanocages for Photoactivatable Catalytic Activity Regulation. Angew Chem Int Ed Engl 2024; 63:e202404064. [PMID: 38517264 DOI: 10.1002/anie.202404064] [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: 02/28/2024] [Indexed: 03/23/2024]
Abstract
DNAzymes exhibit tremendous application potentials in the field of biosensing and gene regulation due to its unique catalytic function. However, spatiotemporally controlled regulation of DNAzyme activity remains a daunting challenge, which may cause nonspecific signal leakage or gene silencing of the catalytic systems. Here, we report a photochemical approach via modular weaving active DNAzyme into the skeleton of tetrahedral DNA nanocages (TDN) for light-triggered on-demand liberation of DNAzyme and thus conditional control of gene regulation activity. We demonstrate that the direct encoding of DNAzyme in TDN could improve the biostability of DNAzyme and ensure the delivery efficiency, comparing with the conventional surface anchoring strategy. Furthermore, the molecular weaving of the DNA nanostructures allows remote control of DNAzyme-mediated gene regulation with high spatiotemporal precision of light. In addition, we demonstrate that the approach is applicable for controlled regulation of the gene editing functions of other functional nucleic acids.
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Affiliation(s)
- Hengzhi Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, China
| | - Deyu Yi
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, 30 XueYuan Road, Beijing, 100083, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, 30 XueYuan Road, Beijing, 100083, China
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23
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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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24
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Sorrentino D, Ranallo S, Nakamura E, Franco E, Ricci F. Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors. Angew Chem Int Ed Engl 2024; 63:e202319382. [PMID: 38457363 DOI: 10.1002/anie.202319382] [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: 12/15/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
We present a strategy to control dynamically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be cotranscriptionally regulated (activated or inhibited) through specific RNA molecules produced by rationally designed synthetic genes. The kinetics of our DNA sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling.
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Affiliation(s)
- Daniela Sorrentino
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Simona Ranallo
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Eiji Nakamura
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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25
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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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26
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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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27
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Garcia-Diosa JA, Grundmeier G, Keller A. Effect of DNA Origami Nanostructures on Bacterial Growth. Chembiochem 2024; 25:e202400091. [PMID: 38299762 DOI: 10.1002/cbic.202400091] [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: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/02/2024]
Abstract
DNA origami nanostructures are a powerful tool in biomedicine and can be used to combat drug-resistant bacterial infections. However, the effect of unmodified DNA origami nanostructures on bacteria is yet to be elucidated. With the aim to obtain a better understanding of this phenomenon, the effect of three DNA origami shapes, i.e., DNA origami triangles, six-helix bundles (6HBs), and 24-helix bundles (24HBs), on the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis is investigated. The results reveal that while triangles and 24HBs can be used as a source of nutrients by E. coli and thereby promote population growth, their effect is much smaller than that of genomic single- and double-stranded DNA. However, no effect on E. coli population growth is observed for the 6HBs. On the other hand, B. subtilis does not show any significant changes in population growth when cultured with the different DNA origami shapes or genomic DNA. The detailed effect of DNA origami nanostructures on bacterial growth thus depends on the competence signals and uptake mechanism of each bacterial species, as well as the DNA origami shape. This should be considered in the development of antimicrobial DNA origami nanostructures.
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Affiliation(s)
- Jaime Andres Garcia-Diosa
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
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28
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Paul R, Paul R, Dutta D, Dash J. pH-dependent complex formation with TAR RNA and DNA: application towards logic gates. Analyst 2024; 149:1976-1980. [PMID: 38465447 DOI: 10.1039/d4an00074a] [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: 03/12/2024]
Abstract
Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
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29
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Vallina NS, McRae EKS, Geary C, Andersen ES. An RNA origami robot that traps and releases a fluorescent aptamer. SCIENCE ADVANCES 2024; 10:eadk1250. [PMID: 38507482 PMCID: PMC10954211 DOI: 10.1126/sciadv.adk1250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA robotic devices that both sense, compute, and actuate to obtain enhanced control over molecular processes. Here, we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer," that mechanically traps the fluorescent aptamer, iSpinach. The Traptamer is shown to sense two RNA key strands, acts as a Boolean AND gate, and reversibly controls the fluorescence of the iSpinach aptamer. Cryo-electron microscopy of the closed Traptamer structure at 5.45-angstrom resolution reveals the mechanical mode of distortion of the iSpinach motif. Our study suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA machines that through sensing, computing, and actuation modules can be used to precisely control RNA functionalities in cellular systems.
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Affiliation(s)
| | - Ewan K. S. McRae
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave, R10-117, Houston, TX 77030, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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30
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Ratajczyk EJ, Šulc P, Turberfield AJ, Doye JPK, Louis AA. Coarse-grained modeling of DNA-RNA hybrids. J Chem Phys 2024; 160:115101. [PMID: 38497475 DOI: 10.1063/5.0199558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 03/19/2024] Open
Abstract
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA-RNA hydrogen bonding interaction, we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability, we provide three examples of its use-calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.
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Affiliation(s)
- Eryk J Ratajczyk
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - 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
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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31
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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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32
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Wang B, Lu Y. Collective Molecular Machines: Multidimensionality and Reconfigurability. NANO-MICRO LETTERS 2024; 16:155. [PMID: 38499833 PMCID: PMC10948734 DOI: 10.1007/s40820-024-01379-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 03/20/2024]
Abstract
Molecular machines are key to cellular activity where they are involved in converting chemical and light energy into efficient mechanical work. During the last 60 years, designing molecular structures capable of generating unidirectional mechanical motion at the nanoscale has been the topic of intense research. Effective progress has been made, attributed to advances in various fields such as supramolecular chemistry, biology and nanotechnology, and informatics. However, individual molecular machines are only capable of producing nanometer work and generally have only a single functionality. In order to address these problems, collective behaviors realized by integrating several or more of these individual mechanical units in space and time have become a new paradigm. In this review, we comprehensively discuss recent developments in the collective behaviors of molecular machines. In particular, collective behavior is divided into two paradigms. One is the appropriate integration of molecular machines to efficiently amplify molecular motions and deformations to construct novel functional materials. The other is the construction of swarming modes at the supramolecular level to perform nanoscale or microscale operations. We discuss design strategies for both modes and focus on the modulation of features and properties. Subsequently, in order to address existing challenges, the idea of transferring experience gained in the field of micro/nano robotics is presented, offering prospects for future developments in the collective behavior of molecular machines.
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Affiliation(s)
- Bin Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, People's Republic of China.
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33
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Liu X, Feng Z, Ran Z, Zeng Y, Cao G, Li X, Ye H, Wang M, Liang W, He Y. External Stimuli-Responsive Strategies for Surface Modification of Orthopedic Implants: Killing Bacteria and Enhancing Osteogenesis. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38497341 DOI: 10.1021/acsami.3c19149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Bacterial infection and insufficient osteogenic activity are the main causes of orthopedic implant failure. Conventional surface modification methods are difficult to meet the requirements for long-term implant placement. In order to better regulate the function of implant surfaces, especially to improve both the antibacterial and osteogenic activity, external stimuli-responsive (ESR) strategies have been employed for the surface modification of orthopedic implants. External stimuli act as "smart switches" to regulate the surface interactions with bacteria and cells. The balance between antibacterial and osteogenic capabilities of implant surfaces can be achieved through these specific ESR manifestations, including temperature changes, reactive oxygen species production, controlled release of bioactive molecules, controlled release of functional ions, etc. This Review summarizes the recent progress on different ESR strategies (based on light, ultrasound, electric, and magnetic fields) that can effectively balance antibacterial performance and osteogenic capability of orthopedic implants. Furthermore, the current limitations and challenges of ESR strategies for surface modification of orthopedic implants as well as future development direction are also discussed.
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Affiliation(s)
- Xujie Liu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhenzhen Feng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhili Ran
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Yaoxun Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Guining Cao
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Xinyi Li
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Huiling Ye
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Meijing Wang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Wanting Liang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Yan He
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
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34
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Smirnov VV, Drozd VS, Patra CK, Hussein Z, Rybalko DS, Kozlova AV, Nour MAY, Zemerova TP, Kolosova OS, Kalnin AY, El-Deeb AA. Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs. Analyst 2024; 149:1947-1957. [PMID: 38385166 DOI: 10.1039/d3an02178e] [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: 02/23/2024]
Abstract
Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.
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Affiliation(s)
- Viktor V Smirnov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Valerya S Drozd
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Christina K Patra
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Daria S Rybalko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Tatiana P Zemerova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Olga S Kolosova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Faculty of Industrial Drug Technology, Saint Petersburg State Chemical and Pharmaceutical University, 14, lit. A, st. Professor Popov, 197022, St. Petersburg, Russian Federation
| | - Arseniy Y Kalnin
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Institute of Chemistry, Saint Petersburg University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
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35
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Youssef S, Tsang E, Samanta A, Kumar V, Gothelf KV. Reversible Protection and Targeted Delivery of DNA Origami with a Disulfide-Containing Cationic Polymer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2301058. [PMID: 37916910 DOI: 10.1002/smll.202301058] [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: 02/06/2023] [Revised: 10/08/2023] [Indexed: 11/03/2023]
Abstract
DNA nanostructures have considerable biomedical potential as intracellular delivery vehicles as they are highly homogeneous and can be functionalized with high spatial resolution. However, challenges like instability under physiological conditions, limited cellular uptake, and lysosomal degradation limit their use. This paper presents a bio-reducible, cationic polymer poly(cystaminebisacrylamide-1,6-diaminohexane) (PCD) as a reversible DNA origami protector. PCD displays a stronger DNA affinity than other cationic polymers. DNA nanostructures with PCD protection are shielded from low salt conditions and DNase I degradation and show a 40-fold increase in cell-association when linked to targeting antibodies. Confocal microscopy reveals a potential secondary cell uptake mechanism, directly delivering the nanostructures to the cytoplasm. Additionally, PCD can be removed by cleaving its backbone disulfides using the intracellular reductant, glutathione. Finally, the application of these constructs is demonstrated for targeted delivery of a cytotoxic agent to cancer cells, which efficiently decreases their viability. The PCD protective agent that is reported here is a simple and efficient method for the stabilization of DNA origami structures. With the ability to deprotect the DNA nanostructures upon entry of the intracellular space, the possibility for the use of DNA origami in pharmaceutical applications is enhanced.
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Affiliation(s)
- Sarah Youssef
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Emily Tsang
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Anirban Samanta
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Vipin Kumar
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
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36
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Yang S, Bögels BWA, Wang F, Xu C, Dou H, Mann S, Fan C, de Greef TFA. DNA as a universal chemical substrate for computing and data storage. Nat Rev Chem 2024; 8:179-194. [PMID: 38337008 DOI: 10.1038/s41570-024-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.
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Affiliation(s)
- Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Can Xu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
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Wu J, Jiao N, Lin D, Li N, Ma T, Tung S, Cheng W, Wu A, Liu L. Dual-Responsive Nanorobot-Based Marsupial Robotic System for Intracranial Cross-Scale Targeting Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2306876. [PMID: 37899660 DOI: 10.1002/adma.202306876] [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: 07/13/2023] [Revised: 10/27/2023] [Indexed: 10/31/2023]
Abstract
Nanorobots capable of active movement are an exciting technology for targeted therapeutic intervention. However, the extensive motion range and hindrance of the blood-brain barrier impeded their clinical translation in glioblastoma therapy. Here, a marsupial robotic system constructed by integrating chemical/magnetic hybrid nanorobots (child robots) with a miniature magnetic continuum robot (mother robot) for intracranial cross-scale targeting drug delivery is reported. For primary targeting on macroscale, the continuum robot enters the cranial cavity through a minimally invasive channel (e.g., Ommaya device) in the skull and transports the nanorobots to pathogenic regions. Upon circumventing the blood-brain barrier, the released nanorobots perform secondary targeting on microscale to further enhance the spatial resolution of drug delivery. In vitro experiments against primary glioblastoma cells derived from different patients are conducted for personalized treatment guidance. The operation feasibility within organisms is shown in ex vivo swine brain experiments. The biosafety of the treatment system is suggested in in vivo experiments. Owing to the hierarchical targeting method, the targeting rate, targeting accuracy, and treatment efficacy have improved greatly. The marsupial robotic system offers a novel intracranial local therapeutic strategy and constitutes a key milestone in the development of glioblastoma treatment platforms.
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Affiliation(s)
- Junfeng Wu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110016, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Niandong Jiao
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Daojing Lin
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110016, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110016, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianyang Ma
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110022, China
| | - Steve Tung
- Department of Mechanical Engineering, University of Arkansas, Arkansas, 72701, USA
| | - Wen Cheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110022, China
| | - Anhua Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110022, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110016, China
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38
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Emanuelson C, Bardhan A, Deiters A. DNA Logic Gates for Small Molecule Activation Circuits in Cells. ACS Synth Biol 2024; 13:538-545. [PMID: 38306634 PMCID: PMC10877608 DOI: 10.1021/acssynbio.3c00474] [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: 08/02/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/04/2024]
Abstract
DNA-based devices such as DNA logic gates self-assemble into supramolecular structures, as dictated by the sequences of the constituent oligonucleotides and their predictable Watson-Crick base pairing interactions. The programmable nature of DNA-based devices permits the design and implementation of DNA circuits that interact in a dynamic and sequential manner capable of spatially arranging disparate DNA species. Here, we report the application of an activatable fluorescence reporter based on a proximity-driven inverse electron demand Diels-Alder (IEDDA) reaction and its robust integration with DNA strand displacement circuits. In response to specific DNA input patterns, sequential strand displacement reactions are initiated and culminate in the hybridization of two modified DNA strands carrying probes capable of undergoing an IEDDA reaction between a vinyl-ether-caged fluorophore and its reactive partner tetrazine, leading to the activation of fluorescence. This approach provides a major advantage for DNA computing in mammalian cells since circuit degradation does not induce fluorescence, in contrast to traditional fluorophore-quencher designs. We demonstrate the robustness and sensitivity of the reporter by testing its ability to serve as a readout for DNA logic circuits of varying complexity inside cells.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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39
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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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40
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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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41
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Li B, Lu Y, Huang X, Ning Y, Shi Q, Liu J, Liu B. Single Multifunctional Nanocabinets-Based Target-Activated Feedback for Simultaneously Precise Monitoring and Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305777. [PMID: 37797188 DOI: 10.1002/smll.202305777] [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: 07/10/2023] [Revised: 09/21/2023] [Indexed: 10/07/2023]
Abstract
Stimulus-responsive mode is highly desirable for improving the precise monitoring and physiological efficacy of endogenous biomarkers (EB). However, its integrated application for visual detection and therapy is limited by inappropriate use of responsive triggers and poor delivery of EB signal-transducing agents, which remain challenging in simultaneous monitoring and noninvasive therapy of EB and EB-mediated pathological events. Target microRNA (miRNA) as controllable reaction triggers and DNAzyme as signal-transducing agent are proposed to develop target-stimulated multifunctional nanocabinets (MFNCs) for the visual tracking of both miRNA and miRNA-mediated anticancer events. The MFNCs, equipped with a target-discriminating sequence-incorporated DNAzyme motif, can specifically release therapeutic molecules through target-triggered conformational switches, accompanied by transduction signal output. Target detection and molecule release performance are recorded in parallel via reverse dual-signal feedback at the single-molecule level. In addition, the intrinsic thermal-replenishing of the MFNCs leads to tumor ablation without invasive exogenous aids. The system achieves visual target quantification, anticancer molecule real-time tracking, and tumor suppression in vivo and in vitro. This work proposes a new paradigm for precise visual exploration of EB or EB-mediated bio-events and provides a demonstration of efficacious all-in-one detection and therapy based on the target-triggered multifunctional nanosystem.
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Affiliation(s)
- Binxiao Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Yanwei Lu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Yujun Ning
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Qian Shi
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Jianwei Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
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42
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Lee EJ, Gladkov N, Miller JE, Yeates TO. Design of Ligand-Operable Protein-Cages That Open Upon Specific Protein Binding. ACS Synth Biol 2024; 13:157-167. [PMID: 38133598 DOI: 10.1021/acssynbio.3c00383] [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: 12/23/2023]
Abstract
Protein nanocages have diverse applications in medicine and biotechnology, including molecular delivery. However, although numerous studies have demonstrated the ability of protein nanocages to encapsulate various molecular species, limited methods are available for subsequently opening a nanocage for cargo release under specific conditions. A modular platform with a specific protein-target-based mechanism of nanocage opening is notably lacking. To address this important technology gap, we present a new class of designed protein cages, the Ligand-Operable Cage (LOC). LOCs primarily comprise a protein nanocage core and a fused surface binding adaptor. The geometry of the LOC is designed so that binding of a target protein ligand (or multiple copies thereof) to the surface binder is sterically incompatible with retention of the assembled state of the cage. Therefore, the tight binding of a target ligand drives cage disassembly by mass action, subsequently exposing the encapsulated cargo. LOCs are modular; direct substitution of the surface binder sequence can reprogram the nanocage to open in response to any target protein ligand of interest. We demonstrate these design principles using both a natural and a designed protein cage as the core, with different proteins acting as the triggering ligand and with different reporter readouts─fluorescence unquenching and luminescence─for cage disassembly. These developments advance the critical problem of targeted molecular delivery and detection.
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Affiliation(s)
- Eric J Lee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Nika Gladkov
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Justin E Miller
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
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43
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Wang P, Fredj Z, Zhang H, Rong G, Bian S, Sawan M. Blocking Superantigen-Mediated Diseases: Challenges and Future Trends. J Immunol Res 2024; 2024:2313062. [PMID: 38268531 PMCID: PMC10807946 DOI: 10.1155/2024/2313062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/26/2024] Open
Abstract
Superantigens are virulence factors secreted by microorganisms that can cause various immune diseases, such as overactivating the immune system, resulting in cytokine storms, rheumatoid arthritis, and multiple sclerosis. Some studies have demonstrated that superantigens do not require intracellular processing and instated bind as intact proteins to the antigen-binding groove of major histocompatibility complex II on antigen-presenting cells, resulting in the activation of T cells with different T-cell receptor Vβ and subsequent overstimulation. To combat superantigen-mediated diseases, researchers have employed different approaches, such as antibodies and simulated peptides. However, due to the complex nature of superantigens, these approaches have not been entirely successful in achieving optimal therapeutic outcomes. CD28 interacts with members of the B7 molecule family to activate T cells. Its mimicking peptide has been suggested as a potential candidate to block superantigens, but it can lead to reduced T-cell activity while increasing the host's infection risk. Thus, this review focuses on the use of drug delivery methods to accurately target and block superantigens, while reducing the adverse effects associated with CD28 mimic peptides. We believe that this method has the potential to provide an effective and safe therapeutic strategy for superantigen-mediated diseases.
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Affiliation(s)
- Pengbo Wang
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Zina Fredj
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Hongyong Zhang
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Guoguang Rong
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Sumin Bian
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Mohamad Sawan
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
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44
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Kosara S, Singh R, Bhatia D. Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives. NANOSCALE ADVANCES 2024; 6:386-401. [PMID: 38235105 PMCID: PMC10790967 DOI: 10.1039/d3na00692a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.
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Affiliation(s)
- Sanjay Kosara
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
| | - Ramesh Singh
- Department of Mechanical Engineering, Colorado State University Fort Collins CO USA
| | - Dhiraj Bhatia
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
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45
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Chen Z, Cao L, Yun K, Lu J. Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly. ACS Macro Lett 2024; 13:94-98. [PMID: 38176070 DOI: 10.1021/acsmacrolett.3c00680] [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: 01/06/2024]
Abstract
Despite 40 years of development of DNA nanotechnology, the fundamental knowledge of the process of DNA strand assembly into targeted nanostructures remains unclear. Study of the dynamic process, especially the competing hybridizations in kinetic traps, provides insight into DNA assembly. In this study, a system of middle-domain first assembly (MDFA) was proposed to enable oligonucleotides to assemble into a 2D DNA monolayer in a pathway-dependent approach. This system was an ideal case to study the dynamic interactions between competing hybridizations during oligonucleotide assembly. Dynamic study revealed the coexistence of the kinetically trapped dead-end byproduct and target product at the early stage of annealing, followed by transformation of the byproduct into the target product by reverse disassembly, due to the equilibrium of the competing hybridizations increasingly favoring the target product pathway. This study offered a better understanding of the assembly pathway of DNA nanostructures for future design.
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Affiliation(s)
- Zhe Chen
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Lingyan Cao
- Department of Prosthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Jingxiong Lu
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Institute of Medi-X, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, China
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46
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Shen F, Wang H, Liu Z, Sun L. DNA Nanostructures: Self-Adjuvant Carriers for Highly Efficient Subunit Vaccines. Angew Chem Int Ed Engl 2024; 63:e202312624. [PMID: 37737971 DOI: 10.1002/anie.202312624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Subunit vaccines based on antigen proteins or epitopes of pathogens or tumors show advantages in immunological precision and high safety, but are often limited by their low immunogenicity. Adjuvants can boost immune responses by stimulating immune cells or promoting antigen uptake by antigen presenting cells (APCs), yet existing clinical adjuvants struggle in simultaneously achieving these dual functions. Additionally, the spatial organization of antigens might be crucial to their immunogenicity. Hence, superior adjuvants should potently stimulate the immune system, precisely arrange antigens, and effectively deliver antigens to APCs. Recently, precisely organizing and delivering antigens with the unique editability of DNA nanostructures has been proposed, presenting unique abilities in significantly improving the immunogenicity of antigens. In this minireview, we will discuss the principles behind using DNA nanostructures as self-adjuvant carriers and review the latest advancements in this field. The potential and challenges associated with self-adjuvant DNA nanostructures will also be discussed.
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Affiliation(s)
- Fengyun Shen
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 201240, China
| | - Haihan Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Lab Carbon Based Functional Materials and Devices, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Lab Carbon Based Functional Materials and Devices, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Lele Sun
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
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47
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Chen B, Sun H, Zhang J, Xu J, Song Z, Zhan G, Bai X, Feng L. Cell-Based Micro/Nano-Robots for Biomedical Applications: A Review. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304607. [PMID: 37653591 DOI: 10.1002/smll.202304607] [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: 06/01/2023] [Revised: 07/28/2023] [Indexed: 09/02/2023]
Abstract
Micro/nano-robots are powerful tools for biomedical applications and are applied in disease diagnosis, tumor imaging, drug delivery, and targeted therapy. Among the various types of micro-robots, cell-based micro-robots exhibit unique properties because of their different cell sources. In combination with various actuation methods, particularly externally propelled methods, cell-based microrobots have enormous potential for biomedical applications. This review introduces recent progress and applications of cell-based micro/nano-robots. Different actuation methods for micro/nano-robots are summarized, and cell-based micro-robots with different cell templates are introduced. Furthermore, the review focuses on the combination of cell-based micro/nano-robots with precise control using different external fields. Potential challenges, further prospects, and clinical translations are also discussed.
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Affiliation(s)
- Bo Chen
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, China
| | - Hongyan Sun
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, China
| | - Jiaying Zhang
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, China
| | - Junjie Xu
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, China
| | - Zeyu Song
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, China
| | - Guangdong Zhan
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, China
| | - Xue Bai
- School of Biomedical Engineering, Capital Medical University, Beijing, 100069, China
| | - Lin Feng
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, 100191, China
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48
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Wang WX, Douglas TR, Zhang H, Bhattacharya A, Rothenbroker M, Tang W, Sun Y, Jia Z, Muffat J, Li Y, Chou LYT. Universal, label-free, single-molecule visualization of DNA origami nanodevices across biological samples using origamiFISH. NATURE NANOTECHNOLOGY 2024; 19:58-69. [PMID: 37500778 DOI: 10.1038/s41565-023-01449-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 07/29/2023]
Abstract
Structural DNA nanotechnology enables the fabrication of user-defined DNA origami nanostructures (DNs) for biological applications. However, the role of DN design during cellular interactions and subsequent biodistribution remain poorly understood. Current methods for tracking DN fates in situ, including fluorescent-dye labelling, suffer from low sensitivity and dye-induced artifacts. Here we present origamiFISH, a label-free and universal method for the single-molecule fluorescence detection of DNA origami nanostructures in cells and tissues. origamiFISH targets pan-DN scaffold sequences with hybridization chain reaction probes to achieve 1,000-fold signal amplification. We identify cell-type- and DN shape-specific spatiotemporal distribution patterns within a minute of uptake and at picomolar DN concentrations, 10,000× lower than field standards. We additionally optimize compatibility with immunofluorescence and tissue clearing to visualize DN distribution within tissue cryo-/vibratome sections, slice cultures and whole-mount organoids. Together, origamiFISH enables the accurate mapping of DN distribution across subcellular and tissue barriers for guiding the development of DN-based therapeutics.
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Affiliation(s)
- Wendy Xueyi Wang
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Travis R Douglas
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Haiwang Zhang
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Afrin Bhattacharya
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Wentian Tang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Yu Sun
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Zhengping Jia
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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49
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Krishnamurthy K, Rajendran A, Nakata E, Morii T. Near Quantitative Ligation Results in Resistance of DNA Origami Against Nuclease and Cell Lysate. SMALL METHODS 2024; 8:e2300999. [PMID: 37736703 DOI: 10.1002/smtd.202300999] [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: 08/04/2023] [Indexed: 09/23/2023]
Abstract
There have been limited efforts to ligate the staple nicks in DNA origami which is crucial for their stability against thermal and mechanical treatments, and chemical and biological environments. Here, two near quantitative ligation methods are demonstrated for the native backbone linkage at the nicks in origami: i) a cosolvent dimethyl sulfoxide (DMSO)-assisted enzymatic ligation and ii) enzyme-free chemical ligation by CNBr. Both methods achieved over 90% ligation in 2D origami, only CNBr-method resulted in ≈80% ligation in 3D origami, while the enzyme-alone yielded 31-55% (2D) or 22-36% (3D) ligation. Only CNBr-method worked efficiently for 3D origami. The CNBr-mediated reaction is completed within 5 min, while DMSO-method took overnight. Ligation by these methods improved the structural stability up to 30 °C, stability during the electrophoresis and subsequent extraction, and against nuclease and cell lysate. These methods are straightforward, non-tedious, and superior in terms of cost, reaction time, and efficiency.
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Affiliation(s)
| | - Arivazhagan Rajendran
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
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50
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Rudchenko S, Taylor S, Milosavic N, Rudchenko M, Wedderhoff Tissi B, Mapara MY, Stojanovic MN. Amplification of Signal on Cell Surfaces in Molecular Cascades. Cells 2023; 12:2858. [PMID: 38132177 PMCID: PMC10742280 DOI: 10.3390/cells12242858] [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: 11/08/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
We can formulate mixtures of oligonucleotide-antibody conjugates to act as molecular cascade-based automata that analyze pairs of cell surface markers (CD markers) on individual cells in a manner consistent with the implementation of Boolean logic-for example, by producing a fluorescent label only if two markers are present. While traditional methods to characterize cells are based on transducing signals from individual cell surface markers, these cascades can be used to combine into a single signal the presence of two or even more CDs. In our original design, oligonucleotide components irreversibly flowed from one antibody to another, driven by increased hybridizations, leading to the magnitude of the final signal on each cell being determined by the surface marker that was the least abundant. This is a significant limitation to the precise labeling of narrow subpopulations, and, in order to overcome it, we changed our design to accomplish signal amplification to a more abundant cell surface marker. We show the AMPLIFY function on two examples: (1) we amplify the fluorescent label from the CD19 marker onto a fivefold more abundant CD45, and (2) we amplify broadly distributed CD45RA to a more constant marker, CD3. We expect this new function to enable the increasingly complex Boolean analysis of cell surfaces.
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Affiliation(s)
- Sergei Rudchenko
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
| | - Steven Taylor
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
| | - Nenad Milosavic
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
| | - Maria Rudchenko
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
| | - Betina Wedderhoff Tissi
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
- Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Markus Y. Mapara
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
| | - Milan N. Stojanovic
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
- Department of Biomedical Engineering, Columbia University, 630W 168th St., Box 84, New York, NY 10032, USA
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