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Fan Y, Li J, Jiang M, Zhao J, He L, Wang Y, Shao F. Self-assembly of DNA G-quadruplex nanowires: a study of the mechanism towards micrometer length. NANOSCALE 2024. [PMID: 39235476 DOI: 10.1039/d4nr02696a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
The G-quadruplex (GQ) formed by guanine-rich DNA strands exhibits superior thermal stability and electric properties, which have generated substantial interest in applying GQ DNA to bioelectric interfaces. However, single G-wires formed by GQs have not yet surpassed the μm length due to the lack of an optimal assembly protocol and understanding of assembly mechanisms that limit application. Herein, we optimized a self-assembly protocol for a short 4-nt oligonucleotide (dG4) to achieve micrometer lengths of G-wires, including the buffer composition, incubation process and surface assembly. Furthermore, both theoretical modeling and chemical modifications were applied to unveil the atomic-level detail of GQ monomer interfaces and indicated that the assembly process follows a stepwise mechanism from nucleation to grow into oligomers and nanowires.
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Affiliation(s)
- Yiqi Fan
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
- Department of Chemistry, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Jiachen Li
- College of Life Sciences, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Min Jiang
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
| | - Jing Zhao
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
- Department of Chemistry, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Lei He
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Fangwei Shao
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
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2
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Li C, He T, Yang X, Feng C, Zhang Z, Zhu J, Dong S, Shi Y, Wei Z, Jiao H, Zhang Y, Liu H, Wang Z, Cheng X. Enhanced Circular Dichroism for Achiral Sensing Based on a DNA-Origami-Empowered Anapole Metasurface. NANO LETTERS 2024; 24:9451-9458. [PMID: 38976602 DOI: 10.1021/acs.nanolett.4c01735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Circular dichroism (CD) spectroscopy has been extensively utilized for detecting and distinguishing the chirality of diverse substances and structures. However, CD spectroscopy is inherently weak and conventionally associated with chiral sensing, thus constraining its range of applications. Here, we report a DNA-origami-empowered metasurface sensing platform through the collaborative effect of metasurfaces and DNA origami, enabling achiral/slightly chiral sensing with high sensitivity via the enhanced ΔCD. An anapole metasurface, boasting over 60 times the average optical chirality enhancement, was elaborately designed to synergize with reconfigurable DNA origami. We experimentally demonstrated the detection of achiral/slightly chiral DNA linker strands via the enhanced ΔCD of the proposed platform, whose sensitivity was a 10-fold enhancement compared with the platform without metasurfaces. Our work presents a high-sensitivity platform for achiral/slightly chiral sensing through chiral spectroscopy, expanding the capabilities of chiral spectroscopy and inspiring the integration of multifunctional artificial nanostructures across diverse domains.
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Affiliation(s)
- Chengfeng Li
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Tao He
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Xu Yang
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Chao Feng
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Zhanyi Zhang
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Jingyuan Zhu
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Siyu Dong
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Yuzhi Shi
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Zeyong Wei
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Hongfei Jiao
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Yinan Zhang
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Huajie Liu
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhanshan Wang
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
| | - Xinbin Cheng
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Professional Technical Service Platform for Full-Spectrum and High-Performance Optical Thin Film Devices and Applications, Shanghai 200092, China
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3
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Wu L, Tanwar S, Kaur G, Date S, Goel L, Chatterjee A, McGuiggan P, Barman I. DNA Origami-Engineered Plasmonic Nanoprobes for Targeted Cancer Imaging. ADVANCED FUNCTIONAL MATERIALS 2024; 34:2309929. [PMID: 39131199 PMCID: PMC11309351 DOI: 10.1002/adfm.202309929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Indexed: 08/13/2024]
Abstract
Plasmonic nanomaterials bearing targeting ligands are of great interest for surface-enhanced Raman scattering (SERS)-based bioimaging applications. However, the practical utility of SERS-based imaging strategies has been hindered by the lack of a straightforward method to synthesize highly sensitive SERS-active nanostructures with high yield and efficiency. In this work, leveraging DNA origami principles, we report the first-in-class design of a SERS-based plasmonically coupled nanoprobe for targeted cancer imaging (SPECTRA). The nanoprobe harnesses a cancer cell targeting DNA aptamer sequence and vibrational tag with stretching frequency in the cell-silent Raman window. Through the integration of aptamer sequence specific for DU145 cells, we show the unique capabilities of SPECTRA for targeted imaging of DU145 cells. Our results demonstrate that the scalability, cost-effectiveness, and reproducibility of this method of fabrication of SERS nanoprobes can serve as a versatile platform for creating nanoprobes with broad applications in the fields of cancer biology and biomedical imaging.
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Affiliation(s)
- Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Swati Tanwar
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Gagandeep Kaur
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Siddhi Date
- Department of Biomedical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Linika Goel
- Department of Biomedical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Arnab Chatterjee
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Patty McGuiggan
- Department of Material Science and Engineering, Johns Hopkins University, Maryland 21218, USA
- Department of Chemistry, Johns Hopkins University, Maryland 21218, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Maryland 21205, USA
- Department of Oncology, Johns Hopkins University, Maryland 21231, USA
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4
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Pang C, Karlinsey BT, Ward M, Harrison RG, Davis RC, Woolley AT. DNA-Templated Nanofabrication of CdS-Au Nanoscale Schottky Contacts and Electrical Characterization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:14076-14085. [PMID: 38934899 DOI: 10.1021/acs.langmuir.4c01554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
DNA-templated nanofabrication presents an innovative approach to creating self-assembled nanoscale metal-semiconductor-based Schottky contacts, which can advance nanoelectronics. Herein, we report the successful fabrication of metal-semiconductor Schottky contacts using a DNA origami scaffold. The scaffold, consisting of DNA strands organized into a specific linear architecture, facilitates the competitive arrangement of Au and CdS nanorods, forming heterojunctions, and addresses previous limitations in low electrical conductance making DNA-templated electronics with semiconductor nanomaterials. Electroless gold plating extends the Au nanorods and makes the necessary electrical contacts. Tungsten electrical connection lines are further created by electron beam-induced deposition. Electrical characterization reveals nonlinear Schottky barrier behavior, with electrical conductance ranging from 0.5 × 10-4 to 1.7 × 10-4 S. The conductance of these DNA-templated junctions is several million times higher than with our prior Schottky contacts. Our research establishes an innovative self-assembly approach with applicable metal and semiconductor materials for making highly conductive nanoscale Schottky contacts, paving the way for the future development of DNA-based nanoscale electronics.
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Affiliation(s)
- Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Benjamin T Karlinsey
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Megan Ward
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Roger G Harrison
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Robert C Davis
- Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, United States
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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5
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Krishnan R S, Firzan Ca N, Mahendran KR. Functionally Active Synthetic α-Helical Pores. Acc Chem Res 2024; 57:1790-1802. [PMID: 38875523 DOI: 10.1021/acs.accounts.4c00101] [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: 06/16/2024]
Abstract
ConspectusTransmembrane pores are currently at the forefront of nanobiotechnology, nanopore chemistry, and synthetic chemical biology research. Over the past few decades, significant studies in protein engineering have paved the way for redesigning membrane protein pores tailored for specific applications in nanobiotechnology. Most previous efforts predominantly centered on natural β-barrel pores designed with atomic precision for nucleic acid sequencing and sensing of biomacromolecules, including protein fragments. The requirement for a more efficient single-molecule detection system has driven the development of synthetic nanopores. For example, engineering channels to conduct ions and biomolecules selectively could lead to sophisticated nanopore sensors. Also, there has been an increased interest in synthetic pores, which can be fabricated to provide more control in designing architecture and diameter for single-molecule sensing of complex biomacromolecules. There have been impressive advancements in developing synthetic DNA-based pores, although their application in nanopore technology is limited. This has prompted a significant shift toward building synthetic transmembrane α-helical pores, a relatively underexplored field offering novel opportunities. Recently, computational tools have been employed to design and construct α-helical barrels of defined structure and functionality.We focus on building synthetic α-helical pores using naturally occurring transmembrane motifs of membrane protein pores. Our laboratory has developed synthetic α-helical transmembrane pores based on the natural porin PorACj (Porin A derived from Corynebacterium jeikeium) that function as nanopore sensors for single-molecule sensing of cationic cyclodextrins and polypeptides. Our breakthrough lies in being the first to create a functional and large stable synthetic transmembrane pore composed of short synthetic α-helical peptides. The key highlight of our work is that these pores can be synthesized using easy chemical synthesis, which permits its easy modification to include a variety of functional groups to build charge-selective sophisticated pores. Additionally, we have demonstrated that stable functional pores can be constructed from D-amino acid peptides. The analysis of pores composed of D- and L-amino acids in the presence of protease showed that only the D pores are highly functional and stable. The structural models of these pores revealed distinct surface charge conformation and geometry. These new classes of synthetic α-helical pores are highly original systems of general interest due to their unique architecture, functionality, and potential applications in nanopore technology and chemical biology. We emphasize that these simplified transmembrane pores have the potential to be components of functional nanodevices and therapeutic tools. We also suggest that such designed peptides might be valuable as antimicrobial agents and can be targeted to cancer cells. This article will focus on the evolutions in assembling α-helical transmembrane pores and highlight their advantages, including structural and functional versatility.
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Affiliation(s)
- Smrithi Krishnan R
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India-695014
| | - Neilah Firzan Ca
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India-695014
- Manipal Academy of Higher Education, Manipal, Karnataka India-576104
| | - Kozhinjampara R Mahendran
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India-695014
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6
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Yuan C, Zhou F, Xu Z, Wu D, Hou P, Yang D, Pan L, Wang P. Functionalized DNA Origami-Enabled Detection of Biomarkers. Chembiochem 2024; 25:e202400227. [PMID: 38700476 DOI: 10.1002/cbic.202400227] [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: 03/12/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/05/2024]
Abstract
Biomarkers are crucial physiological and pathological indicators in the host. Over the years, numerous detection methods have been developed for biomarkers, given their significant potential in various biological and biomedical applications. Among these, the detection system based on functionalized DNA origami has emerged as a promising approach due to its precise control over sensing modules, enabling sensitive, specific, and programmable biomarker detection. We summarize the advancements in biomarker detection using functionalized DNA origami, focusing on strategies for DNA origami functionalization, mechanisms of biomarker recognition, and applications in disease diagnosis and monitoring. These applications are organized into sections based on the type of biomarkers - nucleic acids, proteins, small molecules, and ions - and concludes with a discussion on the advantages and challenges associated with using functionalized DNA origami systems for biomarker detection.
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Affiliation(s)
- Caiqing Yuan
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Zhou
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zhihao Xu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Dunkai Wu
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Hou
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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7
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Li L, Yin J, Ma W, Tang L, Zou J, Yang L, Du T, Zhao Y, Wang L, Yang Z, Fan C, Chao J, Chen X. A DNA origami device spatially controls CD95 signalling to induce immune tolerance in rheumatoid arthritis. NATURE MATERIALS 2024; 23:993-1001. [PMID: 38594486 DOI: 10.1038/s41563-024-01865-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
DNA origami is capable of spatially organizing molecules into sophisticated geometric patterns with nanometric precision. Here we describe a reconfigurable, two-dimensional DNA origami with geometrically patterned CD95 ligands that regulates immune cell signalling to alleviate rheumatoid arthritis. In response to pH changes, the device reversibly transforms from a closed to an open configuration, displaying a hexagonal pattern of CD95 ligands with ~10 nm intermolecular spacing, precisely mirroring the spatial arrangement of CD95 receptor clusters on the surface of immune cells. In a collagen-induced arthritis mouse model, DNA origami elicits robust and selective activation of CD95 death-inducing signalling in activated immune cells located in inflamed synovial tissues. Such localized immune tolerance ameliorates joint damage with no noticeable side effects. This device allows for the precise spatial control of cellular signalling, expanding our understanding of ligand-receptor interactions and is a promising platform for the development of pharmacological interventions targeting these interactions.
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Affiliation(s)
- Ling Li
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Jue Yin
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Wen Ma
- Strait Laboratory of Flexible Electronics, Fujian Key Laboratory of Flexible Electronics, Strait Institute of Flexible Electronics, Fujian Normal University, Fuzhou, China
| | - Longguang Tang
- Department of Pharmacy, Center for Regeneration and Aging Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Jianhua Zou
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Linzi Yang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Ting Du
- West China School of Public Health and West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yi Zhao
- Strait Laboratory of Flexible Electronics, Fujian Key Laboratory of Flexible Electronics, Strait Institute of Flexible Electronics, Fujian Normal University, Fuzhou, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Zhen Yang
- Strait Laboratory of Flexible Electronics, Fujian Key Laboratory of Flexible Electronics, Strait Institute of Flexible Electronics, Fujian Normal University, Fuzhou, China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China.
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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8
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Wei X, Chen C, Popov AV, Bathe M, Hernandez R. Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures. J Phys Chem A 2024; 128:4999-5008. [PMID: 38875485 DOI: 10.1021/acs.jpca.4c02603] [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: 06/16/2024]
Abstract
DNA nanotechnology has broad applications in biomedical drug delivery and programmable materials. Characterization of the self-assembly of DNA origami and quantum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchical nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multimeric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of different multimeric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis.
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Affiliation(s)
- Xingfei Wei
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chi Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander V Popov
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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9
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Teng T, Bernal‐Chanchavac J, Stephanopoulos N, Castro CE. Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled-Coil Patches and Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307257. [PMID: 38459678 PMCID: PMC11132032 DOI: 10.1002/advs.202307257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/22/2023] [Indexed: 03/10/2024]
Abstract
DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence-specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled-coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher-order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled-coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5-10-fold increase in bending stiffness. The results provide a foundation for stimulus-responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
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Affiliation(s)
- Teng Teng
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
| | - Julio Bernal‐Chanchavac
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Nicholas Stephanopoulos
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
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10
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Fan G, Corbin N, Chung M, Gill TM, Moore EB, Karbelkar AA, Furst AL. Highly Efficient Carbon Dioxide Electroreduction via DNA-Directed Catalyst Immobilization. JACS AU 2024; 4:1413-1421. [PMID: 38665653 PMCID: PMC11040669 DOI: 10.1021/jacsau.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
Electrochemical reduction of carbon dioxide (CO2) is a promising route to up-convert this industrial byproduct. However, to perform this reaction with a small-molecule catalyst, the catalyst must be proximal to an electrode surface. Efforts to immobilize molecular catalysts on electrodes have been stymied by the need to optimize the immobilization chemistries on a case-by-case basis. Taking inspiration from nature, we applied DNA as a molecular-scale "Velcro" to investigate the tethering of three porphyrin-based catalysts to electrodes. This tethering strategy improved both the stability of the catalysts and their Faradaic efficiencies (FEs). DNA-catalyst conjugates were immobilized on screen-printed carbon and carbon paper electrodes via DNA hybridization with nearly 100% efficiency. Following immobilization, a higher catalyst stability at relevant potentials is observed. Additionally, lower overpotentials are required for the generation of carbon monoxide (CO). Finally, high FE for CO generation was observed with the DNA-immobilized catalysts as compared to the unmodified small-molecule systems, as high as 79.1% FE for CO at -0.95 V vs SHE using a DNA-tethered catalyst. This work demonstrates the potential of DNA "Velcro" as a powerful strategy for catalyst immobilization. Here, we demonstrated improved catalytic characteristics of molecular catalysts for CO2 valorization, but this strategy is anticipated to be generalizable to any reaction that proceeds in aqueous solutions.
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Affiliation(s)
- Gang Fan
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Nathan Corbin
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Minju Chung
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas M. Gill
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Evan B. Moore
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Amruta A. Karbelkar
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Ariel L. Furst
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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12
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Brisson ERL, Worthington MJH, Kerai S, Müllner M. Nanoscale polymer discs, toroids and platelets: a survey of their syntheses and potential applications. Chem Soc Rev 2024; 53:1984-2021. [PMID: 38173417 DOI: 10.1039/d1cs01114f] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Polymer self-assembly has become a reliable and versatile workhorse to produce polymeric nanomaterials. With appropriate polymer design and monomer selection, polymers can assemble into shapes and morphologies beyond well-studied spherical and cylindrical micellar structures. Steadfast access to anisotropic polymer nanoparticles has meant that the fabrication and application of 2D soft matter has received increasing attention in recent years. In this review, we focus on nanoscale polymer discs, toroids, and platelets: three morphologies that are often interrelated and made from similar starting materials or common intermediates. For each morphology, we illustrate design rules, and group and discuss commonly used self-assembly strategies. We further highlight polymer compositions, fundamental principles and self-assembly conditions that enable precision in bottom-up fabrication strategies. Finally, we summarise potential applications of such nanomaterials, especially in the context of biomedical research and template chemistry and elaborate on future endeavours in this space.
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Affiliation(s)
- Emma R L Brisson
- Key Centre for Polymers and Colloids, School of Chemistry, The University of Sydney, Sydney 2006 NSW, Australia.
| | - Max J H Worthington
- Key Centre for Polymers and Colloids, School of Chemistry, The University of Sydney, Sydney 2006 NSW, Australia.
| | - Simran Kerai
- Key Centre for Polymers and Colloids, School of Chemistry, The University of Sydney, Sydney 2006 NSW, Australia.
| | - Markus Müllner
- Key Centre for Polymers and Colloids, School of Chemistry, The University of Sydney, Sydney 2006 NSW, Australia.
- The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, Sydney 2006 NSW, Australia
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13
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [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: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, 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, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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14
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Sun Z, Ren Y, Zhu W, Xiao Y, Wu H. DNA nanotechnology-based nucleic acid delivery systems for bioimaging and disease treatment. Analyst 2024; 149:599-613. [PMID: 38221846 DOI: 10.1039/d3an01871g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Nucleic acids, including DNA and RNA, have been considered as powerful and functional biomaterials owing to their programmable structure, good biocompatibility, and ease of synthesis. However, traditional nucleic acid-based probes have always suffered from inherent limitations, including restricted cell internalization efficiency and structural instability. In recent years, DNA nanotechnology has shown great promise for the applications of bioimaging and drug delivery. The attractive superiorities of DNA nanostructures, such as precise geometries, spatial addressability, and improved biostability, have enabled them to be a novel category of nucleic acid delivery systems for biomedical applications. In this review, we introduce the development of DNA nanotechnology, and highlight recent advances of DNA nanostructure-based delivery systems for cellular imaging and therapeutic applications. Finally, we propose the challenges as well as opportunities for the future development of DNA nanotechnology in biomedical research.
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Affiliation(s)
- Zhaorong Sun
- Department of Pharmacy, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, Shandong, 271000, China
| | - Yingjie Ren
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Wenjun Zhu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuliang Xiao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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15
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Brannetti S, Gentile S, Chamorro-Garcia A, Barbero L, Del Grosso E, Ricci F. Decorated DNA-Based Scaffolds as Lateral Flow Biosensors. Angew Chem Int Ed Engl 2023; 62:e202313243. [PMID: 37804080 DOI: 10.1002/anie.202313243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/08/2023]
Abstract
Here we develop Lateral Flow Assays (LFAs) that employ as functional elements DNA-based structures decorated with reporter tags and recognition elements. We have rationally re-engineered tile-based DNA tubular structures that can act as scaffolds and can be decorated with recognition elements of different nature (i.e. antigens, aptamers or proteins) and with orthogonal fluorescent dyes. As a proof-of-principle we have developed sandwich and competitive multiplex lateral flow platforms for the detection of several targets, ranging from small molecules (digoxigenin, Dig and dinitrophenol, DNP), to antibodies (Anti-Dig, Anti-DNP and Anti-MUC1/EGFR bispecific antibodies) and proteins (thrombin). Coupling the advantages of functional DNA-based scaffolds together with the simplicity of LFAs, our approach offers the opportunity to detect a wide range of targets with nanomolar sensitivity and high specificity.
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Affiliation(s)
- Simone Brannetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Serena Gentile
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alejandro Chamorro-Garcia
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Luca Barbero
- RBM-Merck an affiliate of Merck KGaA, Via Ribes 1, 10010, Turin, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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16
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McCarthy DR, Remington JM, Ferrell JB, Schneebeli ST, Li J. Nano-Bio Interactions between DNA Nanocages and Human Serum Albumin. J Chem Theory Comput 2023; 19:7873-7881. [PMID: 37877553 PMCID: PMC11070245 DOI: 10.1021/acs.jctc.3c00720] [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] [Indexed: 10/26/2023]
Abstract
DNA nanostructures have emerged as promising nanomedical tools due to their biocompatibility and tunable behavior. Recent work has shown that DNA nanocages decorated with organic dendrimers strongly bind human serum albumin (HSA), yet the dynamic structures of these complexes remain uncharacterized. This theoretical and computational investigation elucidates the fuzzy interactions between dendritically functionalized cubic DNA nanocages and HSA. The dendrimer-HSA interactions occur via nonspecific binding with the protein thermodynamically and kinetically free to cross the open faces of the cubic scaffold. However, the rigidity of the DNA scaffold prevents the binding energetics from scaling with the number of dendrimers. These discoveries not only provide a useful framework by which to model general interactions of DNA nanostructures complexed with serum proteins but also give valuable molecular insight into the design of next-generation DNA nanomedicines.
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Affiliation(s)
| | | | | | - Severin T. Schneebeli
- Department of Chemistry, University of Vermont, Burlington, VT 05405
- Department of Industrial and Physical Pharmacy and Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT 05405
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
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17
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Joseph N, Shapiro A, Gillis E, Barkey S, Abu-Horowitz A, Bachelet I, Mizrahi B. Biodistribution and function of coupled polymer-DNA origami nanostructures. Sci Rep 2023; 13:19567. [PMID: 37949918 PMCID: PMC10638432 DOI: 10.1038/s41598-023-46351-1] [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: 01/16/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Spatial control over the distribution of therapeutics is a highly desired feature, which could limit the side effects of many drugs. Here we describe a nanoscale agent, fabricated from a coupled polymer-DNA origami hybrid that exhibits stability in serum and slow diffusion through tissues, in a manner correlating with shape and aspect ratio. Coupling to fragments of polyethylene glycol (PEG) through polyamine electrostatic interactions resulted in marked stability of the agents in-vivo, with > 90% of the agents maintaining structural integrity 5 days following subcutaneous injection. An agent functionalized with aptamers specific for human tumor necrosis factor TNF-alpha, significantly abrogated the inflammatory response in a delayed-type hypersensitivity model in humanized TNF-alpha mice. These findings highlight polymer-DNA hybrid nanostructures as a programmable and pharmacologically viable update to mainstream technologies such as monoclonal antibodies, capable of exerting an additional layer of control across the spatial dimension of drug activity.
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Affiliation(s)
- Noah Joseph
- Augmanity Nano Ltd., 7670308, Rehovot, Israel
| | - Anastasia Shapiro
- Augmanity Nano Ltd., 7670308, Rehovot, Israel.
- Faculty of Biotechnology and Food Engineering, 32000, Technion, Haifa, Israel.
| | - Ella Gillis
- Augmanity Nano Ltd., 7670308, Rehovot, Israel
| | | | | | | | - Boaz Mizrahi
- Faculty of Biotechnology and Food Engineering, 32000, Technion, Haifa, Israel
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18
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Fokina A, Poletaeva Y, Dukova S, Klabenkova K, Rad’kova Z, Bakulina A, Zatsepin T, Ryabchikova E, Stetsenko D. Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides. Int J Mol Sci 2023; 24:15978. [PMID: 37958961 PMCID: PMC10650595 DOI: 10.3390/ijms242115978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.
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Affiliation(s)
- Alesya Fokina
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yulia Poletaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (Y.P.); (E.R.)
| | | | - Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Zinaida Rad’kova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia; (Z.R.); (A.B.)
| | - Anastasia Bakulina
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia; (Z.R.); (A.B.)
| | - Timofei Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (Y.P.); (E.R.)
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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19
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Zhang L, Zhao H, Yang H, Su X. Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection. Biosens Bioelectron 2023; 239:115622. [PMID: 37611449 DOI: 10.1016/j.bios.2023.115622] [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: 05/29/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
DNA-based enzyme-free signal amplification strategies are widely employed to detect biomarkers in low abundance. To enhance signal amplification, localized DNA reaction units which increases molecular collision probability is commonly utilized. However, the current understanding of the structure-function relationships in localized DNA signal amplification probes is limited, leading to unsatisfied performance. In this study, we introduced a coarse-grained molecular model to simulate the dynamic behavior of two DNA reaction units within a DNA enzyme-free signal amplification circuit called Localized Catalytic Hairpin Assembly (LCHA). We investigated the impact of localized distance and flexibility on reaction performance. The most efficient LCHA probe guided by simulation exhibits sensitivity 28 times greater that of free CHA, with a detection limit of miR-21 reaching 16 pM, while the least effective LCHA probe demonstrated a modest improvement of only 7 times. We successfully employed the optimized probe to differentiate cancer cells from normal cells based on their miR-21 expression levels, showcasing its quantification ability. By elucidating the mechanistic insights and structure-function relationship in our work, we aim to contribute valuable information that can save users' time and reduce costs when designing localized DNA probes. With a comprehensive understanding of how the localization affects probe performance, researchers can now make more informed and efficient decisions during the design process. This work would find broad applications of DNA nanotechnology in biosensing, biocomputing, and bionic robots.
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Affiliation(s)
- Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hongyang Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huixiao Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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20
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Richter L, Szalai AM, Manzanares-Palenzuela CL, Kamińska I, Tinnefeld P. Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303152. [PMID: 37670535 DOI: 10.1002/adma.202303152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/31/2023] [Indexed: 09/07/2023]
Abstract
The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.
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Affiliation(s)
- Lars Richter
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - Alan M Szalai
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - C Lorena Manzanares-Palenzuela
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - Izabela Kamińska
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
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21
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Teng T, Bernal-Chanchavac J, Stephanopoulos N, Castro CE. Construction and reconfiguration of dynamic DNA origami assemblies with coiled-coil patches and patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559112. [PMID: 37790447 PMCID: PMC10542533 DOI: 10.1101/2023.09.23.559112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structure and properties. Here we report the integration of DNA origami hinge nanodevices and coiled-coil peptides into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, we make multiple higher order assemblies by organizing clusters of peptides (i.e. patches) or arranging single peptides (i.e. patterns) on the surfaces of DNA origami to control the relative orientation of devices. We use coiled-coil interactions to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based actuation. Actuation of linear assemblies leads to micron scale motions and ~2.5-10-fold increase in bending stiffness. Our results provide a foundation for stimulus responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
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Affiliation(s)
- T Teng
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, United States
| | - J Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - N Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - C E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, United States
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22
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Li S, Shi B, He D, Zhou H, Gao Z. DNA origami-mediated plasmonic dimer nanoantenna-based SERS biosensor for ultrasensitive determination of trace diethylstilbestrol. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131874. [PMID: 37379602 DOI: 10.1016/j.jhazmat.2023.131874] [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: 01/12/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Diethylstilbestrol (DES) is a threatening factor to the human endocrine system. Here, we reported a DNA origami-assembled plasmonic dimer nanoantenna-based surface-enhanced Raman scattering (SERS) biosensor for measuring trace DES in foods. A critical factor influencing the SERS effect is interparticle gap modulation of SERS hotspots with nanometer-scale accuracy. DNA origami technology aims to generate naturally perfect structures with nano-scale precision. Exploiting the specificity of base-pairing and spatial addressability of DNA origami to form plasmonic dimer nanoantenna, the designed SERS biosensor generated electromagnetic-enhancement and uniform-enhancement hotspots to improve sensitivity and uniformity. Owing to their high target-binding affinity, aptamer-functionalized DNA origami biosensors transduced the target recognition into dynamic structural transformations of plasmonic nanoantennas, which were further converted to amplified Raman outputs. A broad linear range from 10-10 to 10-5 M was obtained with the detection limit of 0.217 nM. Our findings demonstrate the utility of aptamer-integrated DNA origami-based biosensors as a promising approach for trace analysis of environmental hazards.
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Affiliation(s)
- Sen Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Naval Logistics Academy, Tianjin 300451, China
| | - Baodi Shi
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Defu He
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Huanying Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
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23
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Oh CY, Henderson ER. In vitro transcription of self-assembling DNA nanoparticles. Sci Rep 2023; 13:12961. [PMID: 37563161 PMCID: PMC10415316 DOI: 10.1038/s41598-023-39777-0] [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: 01/26/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Nucleic acid nanoparticles are playing an increasingly important role in biomolecular diagnostics and therapeutics as well as a variety of other areas. The unique attributes of self-assembling DNA nanoparticles provide a potentially valuable addition or alternative to the lipid-based nanoparticles that are currently used to ferry nucleic acids in living systems. To explore this possibility, we have assessed the ability of self-assembling DNA nanoparticles to be constructed from complete gene cassettes that are capable of gene expression in vitro. In the current report, we describe the somewhat counter-intuitive result that despite extensive crossovers (the stereochemical analogs of Holliday junctions) and variations in architecture, these DNA nanoparticles are amenable to gene expression as evidenced by T7 RNA polymerase-driven transcription of a reporter gene in vitro. These findings, coupled with the vastly malleable architecture and chemistry of self-assembling DNA nanoparticles, warrant further investigation of their utility in biomedical genetics.
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Affiliation(s)
- Chang Yong Oh
- Department of Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Eric R Henderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
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24
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Rodríguez-Franco HJ, Weiden J, Bastings MMC. Stabilizing Polymer Coatings Alter the Protein Corona of DNA Origami and Can Be Engineered to Bias the Cellular Uptake. ACS POLYMERS AU 2023; 3:344-353. [PMID: 37576710 PMCID: PMC10416322 DOI: 10.1021/acspolymersau.3c00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 08/15/2023]
Abstract
With DNA-based nanomaterials being designed for applications in cellular environments, the need arises to accurately understand their surface interactions toward biological targets. As for any material exposed to protein-rich cell culture conditions, a protein corona will establish around DNA nanoparticles, potentially altering the a-priori designed particle function. Here, we first set out to identify the protein corona around DNA origami nanomaterials, taking into account the application of stabilizing block co-polymer coatings (oligolysine-1kPEG or oligolysine-5kPEG) widely used to ensure particle integrity. By implementing a label-free methodology, the distinct polymer coating conditions show unique protein profiles, predominantly defined by differences in the molecular weight and isoelectric point of the adsorbed proteins. Interestingly, none of the applied coatings reduced the diversity of the proteins detected within the specific coronae. We then biased the protein corona through pre-incubation with selected proteins and show significant changes in the cell uptake. Our study contributes to a deeper understanding of the complex interplay between DNA nanomaterials, proteins, and cells at the bio-interface.
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Affiliation(s)
- Hugo J. Rodríguez-Franco
- Programmable Biomaterials Laboratory,
Institute of Materials, Interfaculty Bioengineering Institute, School
of Engineering, Ecole Polytechnique Fédérale
Lausanne, Lausanne 1015, Switzerland
| | - Jorieke Weiden
- Programmable Biomaterials Laboratory,
Institute of Materials, Interfaculty Bioengineering Institute, School
of Engineering, Ecole Polytechnique Fédérale
Lausanne, Lausanne 1015, Switzerland
| | - Maartje M. C. Bastings
- Programmable Biomaterials Laboratory,
Institute of Materials, Interfaculty Bioengineering Institute, School
of Engineering, Ecole Polytechnique Fédérale
Lausanne, Lausanne 1015, Switzerland
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25
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Tang Y, Liu H, Wang Q, Qi X, Yu L, Šulc P, Zhang F, Yan H, Jiang S. DNA Origami Tessellations. J Am Chem Soc 2023. [PMID: 37329284 DOI: 10.1021/jacs.3c03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami nanostructures are excellent building blocks for constructing tessellation patterns. However, the size and complexity of DNA origami tessellation systems are currently limited by several unexplored factors relevant to the accuracy of essential design parameters, the applicability of design strategies, and the compatibility between different tiles. Here, we present a general method for creating DNA origami tiles that grow into tessellation patterns with micrometer-scale order and nanometer-scale precision. Interhelical distance (D) was identified as a critical design parameter determining tile conformation and tessellation outcome. Finely tuned D facilitated the accurate geometric design of monomer tiles with minimized curvature and improved tessellation capability, enabling the formation of single-crystalline lattices ranging from tens to hundreds of square micrometers. The general applicability of the design method was demonstrated by 9 tile geometries, 15 unique tile designs, and 12 tessellation patterns covering Platonic, Laves, and Archimedean tilings. Particularly, we took two strategies to increase the complexity of DNA origami tessellation, including reducing the symmetry of monomer tiles and coassembling tiles of different geometries. Both yielded various tiling patterns that rivaled Platonic tilings in size and quality, indicating the robustness of the optimized tessellation system. This study will promote DNA-templated, programmable molecular and material patterning and open up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
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Affiliation(s)
- Yue Tang
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaodong Qi
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Lu Yu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Fei Zhang
- Department of Chemistry, School of Arts & Sciences-Newark, Rutgers University, Newark, New Jersey 07102, United States
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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26
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Oktay E, Bush J, Vargas M, Scarton DV, O'Shea B, Hartman A, Green CM, Neyra K, Gomes CM, Medintz IL, Mathur D, Veneziano R. Customized Scaffolds for Direct Assembly of Functionalized DNA Origami. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37267624 DOI: 10.1021/acsami.3c05690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Functional DNA origami nanoparticles (DNA-NPs) are used as nanocarriers in a variety of biomedical applications including targeted drug delivery and vaccine development. DNA-NPs can be designed into a broad range of nanoarchitectures in one, two, and three dimensions with high structural fidelity. Moreover, the addressability of the DNA-NPs enables the precise organization of functional moieties, which improves targeting, actuation, and stability. DNA-NPs are usually functionalized via chemically modified staple strands, which can be further conjugated with additional polymers and proteins for the intended application. Although this method of functionalization is extremely efficient to control the stoichiometry and organization of functional moieties, fewer than half of the permissible sites are accessible through staple modifications. In addition, DNA-NP functionalization rapidly becomes expensive when a high number of functionalizations such as fluorophores for tracking and chemical modifications for stability that do not require spatially precise organization are used. To facilitate the synthesis of functional DNA-NPs, we propose a simple and robust strategy based on an asymmetric polymerase chain reaction (aPCR) protocol that allows direct synthesis of custom-length scaffolds that can be randomly modified and/or precisely modified via sequence design. We demonstrated the potential of our strategy by producing and characterizing heavily modified scaffold strands with amine groups for dye functionalization, phosphorothioate bonds for stability, and biotin for surface immobilization. We further validated our sequence design approach for precise conjugation of biomolecules by synthetizing scaffolds including binding loops and aptamer sequences that can be used for direct hybridization of nucleic acid tagged biomolecules or binding of protein targets.
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Affiliation(s)
- Esra Oktay
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Joshua Bush
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Merlyn Vargas
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Dylan Valerio Scarton
- College of Science, Interdisciplinary Program in Neuroscience, George Mason University, Fairfax, Virginia 22030-4444, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Bailey O'Shea
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Amber Hartman
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Carolina M Gomes
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Remi Veneziano
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
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27
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Zhang Y, Yang D, Wang P, Ke Y. Building Large DNA Bundles via Controlled Hierarchical Assembly of DNA Tubes. ACS NANO 2023. [PMID: 37207344 DOI: 10.1021/acsnano.3c01342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology is capable of fabricating designer nanoscale artificial architectures. Developing simple and yet versatile assembly methods to construct large DNA structures of defined spatial features and dynamic capabilities has remained challenging. Herein, we designed a molecular assembly system where DNA tiles can assemble into tubes and then into large one-dimensional DNA bundles following a hierarchical pathway. A cohesive link was incorporated into the tile to induce intertube binding for the formation of DNA bundles. DNA bundles with length of dozens of micrometers and width of hundreds of nanometers were produced, whose assembly was revealed to be collectively determined by cationic strength and linker designs (binding strength, spacer length, linker position, etc.). Furthermore, multicomponent DNA bundles with programmable spatial features and compositions were realized by using various distinct tile designs. Lastly, we implemented dynamic capability into large DNA bundles to realize reversible reconfigurations among tile, tube, and bundles following specific molecular stimulations. We envision this assembly strategy can enrich the toolbox of DNA nanotechnology for rational design of large-size DNA materials of defined features and properties that may be applied to a variety of fields in materials science, synthetic biology, biomedical science, and beyond.
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Affiliation(s)
- Yunlong Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yonggang Ke
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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28
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Parikka JM, Järvinen H, Sokołowska K, Ruokolainen V, Markešević N, Natarajan AK, Vihinen-Ranta M, Kuzyk A, Tapio K, Toppari JJ. Creation of ordered 3D tubes out of DNA origami lattices. NANOSCALE 2023; 15:7772-7780. [PMID: 37057647 DOI: 10.1039/d2nr06001a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hierarchical self-assembly of nanostructures with addressable complexity has been a promising route for realizing novel functional materials. Traditionally, the fabrication of such structures on a large scale has been achievable using top-down methods but with the cost of complexity of the fabrication equipment versus resolution and limitation mainly to 2D structures. More recently bottom-up methods using molecules like DNA have gained attention due to the advantages of low fabrication costs, high resolution and simplicity in an extension of the methods to the third dimension. One of the more promising bottom-up techniques is DNA origami due to the robust self-assembly of arbitrarily shaped nanostructures with feature sizes down to a few nanometers. Here, we show that under specific ionic conditions of the buffer, the employed plus-shaped, blunt-ended Seeman tile (ST) origami forms elongated, ordered 2D lattices, which are further rolled into 3D tubes in solution. Imaging structures on a surface by atomic force microscopy reveals ribbon-like structures, with single or double layers of the origami lattice. Further studies of the double-layered structures in a liquid state by confocal microscopy and cryo-TEM revealed elongated tube structures with a relatively uniform width but with a varying length. Through meticulous study, we concluded that the assembly process of these 3D DNA origami tubes is heavily dependent on the concentration of both mono- and divalent cations. In particular, nickel seems to act as a trigger for the formation of the tubular assemblies in liquid.
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Affiliation(s)
- Johannes M Parikka
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Heini Järvinen
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Karolina Sokołowska
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Visa Ruokolainen
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Nemanja Markešević
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Ashwin K Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Maija Vihinen-Ranta
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Kosti Tapio
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - J Jussi Toppari
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
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29
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Ghosal S, Bag S, Bhowmik S. Unravelling the Drug Encapsulation Ability of Functional DNA Origami Nanostructures: Current Understanding and Future Prospects on Targeted Drug Delivery. Polymers (Basel) 2023; 15:1850. [PMID: 37111997 PMCID: PMC10144338 DOI: 10.3390/polym15081850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023] Open
Abstract
Rapid breakthroughs in nucleic acid nanotechnology have always driven the creation of nano-assemblies with programmable design, potent functionality, good biocompatibility, and remarkable biosafety during the last few decades. Researchers are constantly looking for more powerful techniques that provide enhanced accuracy with greater resolution. The self-assembly of rationally designed nanostructures is now possible because of bottom-up structural nucleic acid (DNA and RNA) nanotechnology, notably DNA origami. Because DNA origami nanostructures can be organized precisely with nanoscale accuracy, they serve as a solid foundation for the exact arrangement of other functional materials for use in a number of applications in structural biology, biophysics, renewable energy, photonics, electronics, medicine, etc. DNA origami facilitates the creation of next-generation drug vectors to help in the solving of the rising demand on disease detection and therapy, as well as other biomedicine-related strategies in the real world. These DNA nanostructures, generated using Watson-Crick base pairing, exhibit a wide variety of properties, including great adaptability, precise programmability, and exceptionally low cytotoxicity in vitro and in vivo. This paper summarizes the synthesis of DNA origami and the drug encapsulation ability of functionalized DNA origami nanostructures. Finally, the remaining obstacles and prospects for DNA origami nanostructures in biomedical sciences are also highlighted.
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Affiliation(s)
- Souvik Ghosal
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to Be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry 607402, India
| | - Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Sudipta Bhowmik
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to Be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry 607402, India
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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30
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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31
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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32
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Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
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Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
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Büber E, Schröder T, Scheckenbach M, Dass M, Franquelim HG, Tinnefeld P. DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout. ACS NANO 2023; 17:3088-3097. [PMID: 36735241 DOI: 10.1021/acsnano.2c11981] [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: 06/18/2023]
Abstract
Particle size is an important characteristic of materials with a direct effect on their physicochemical features. Besides nanoparticles, particle size and surface curvature are particularly important in the world of lipids and cellular membranes as the cell membrane undergoes conformational changes in many biological processes which leads to diverging local curvature values. On account of that, it is important to develop cost-effective, rapid and sufficiently precise systems that can measure the surface curvature on the nanoscale that can be translated to size for spherical particles. As an alternative approach for particle characterization, we present flexible DNA nanodevices that can adapt to the curvature of the structure they are bound to. The curvature sensors use Fluorescence Resonance Energy Transfer (FRET) as the transduction mechanism on the single-molecule level. The curvature sensors consist of segmented DNA origami structures connected via flexible DNA linkers incorporating a FRET pair. The activity of the sensors was first demonstrated with defined binding to different DNA origami geometries used as templates. Then the DNA origami curvature sensors were applied to measure spherical silica beads having different size, and subsequently on lipid vesicles. With the designed sensors, we could reliably distinguish different sized nanoparticles within a size range of 50-300 nm as well as the bending angle range of 50-180°. This study helps with the development of more advanced modular-curvature sensing devices that are capable of determining the sizes of nanoparticles and biological complexes.
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Affiliation(s)
- Ece Büber
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, 80539Munich, Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152Martinsried, Germany
- Interfaculty Centre for Bioactive Matter, Leipzig University, c/o Deutscher Platz 5 (BBZ), 04109Leipzig, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
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Bednarz A, Sønderskov SM, Dong M, Birkedal V. Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures. NANOSCALE 2023; 15:1317-1326. [PMID: 36545884 DOI: 10.1039/d2nr05780h] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nucleic acid-based biomolecular self-assembly enables the creation of versatile functional architectures. Electrostatic screening of the negative charges of nucleic acids is essential for their folding and stability; thus, ions play a critical role in nucleic acid self-assembly in both biology and nanotechnology. However, the ion-DNA interplay and the resulting ion-specific structural integrity and responsiveness of DNA constructs are underexploited. Here, we harness a wide range of mono- and divalent ions to control the structural features of DNA origami constructs. Using atomic force microscopy and Förster resonance energy transfer (FRET) spectroscopy down to the single-molecule level, we report on the global and local structural performance and responsiveness of DNA origami constructs following self-assembly, upon post-assembly ion exchange and post-assembly ion-mediated reconfiguration. We determined the conditions for highly efficient DNA origami folding in the presence of several mono- (Li+, Na+, K+, Cs+) and divalent (Ca2+, Sr2+, Ba2+) ions, expanding the range where DNA origami structures can be exploited for custom-specific applications. We then manipulated fully folded constructs by exposing them to unfavorable ionic conditions that led to the emergence of substantial disintegrity but not to unfolding. Moreover, we found that poorly assembled nanostructures at low ion concentrations undergo substantial self-repair upon ion addition in the absence of free staple strands. This reconfigurability occurs in an ion type- and concentration-specific manner. Our findings provide a fundamental understanding of the ion-mediated structural responsiveness of DNA origami at the nanoscale enabling applications under a wide range of ionic conditions.
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Affiliation(s)
- Aleksandra Bednarz
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark.
| | | | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark.
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35
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He Z, Xiang W, Fan Q, Wang L, Chao J. A DNA origami nanostructure embedded with NQO1-activated prodrugs for precision drug delivery. Chem Commun (Camb) 2023; 59:912-915. [PMID: 36594872 DOI: 10.1039/d2cc06367k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A rectangle DNA origami nanostructure equipped with doxorubicin-derived prodrugs targeting a tumor cell-specific enzyme (NQO1) is constructed. Combining the high prodrug payload of DNA origami and NQO1-activated chemotherapy, this nanosystem presents therapeutic selectivity for NQO1-overexpressing MCF-7 cells over healthy L02 cells, offering a potent strategy for precision cancer therapy.
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Affiliation(s)
- Zhimei He
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing, 210023, P. R. China.
| | - Wenjie Xiang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210023, P. R. China
| | - Qin Fan
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210023, P. R. China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210023, P. R. China
| | - Jie Chao
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing, 210023, P. R. China. .,Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210023, P. R. China
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36
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Marrs J, Lu Q, Pan V, Ke Y, Hihath J. Structure-Dependent Electrical Conductance of DNA Origami Nanowires. Chembiochem 2023; 24:e202200454. [PMID: 36342926 DOI: 10.1002/cbic.202200454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Indexed: 11/09/2022]
Abstract
Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si3 N4 ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si3 N4 substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼1013 ohms) than on native Si3 N4 substrates without HMDS (∼1014 ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si3 N4 substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.
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Affiliation(s)
- Jonathan Marrs
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California, 95616, USA
| | - Qinyi Lu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Victor Pan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California, 95616, USA.,Biodesign Center for Bioelectronics, School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA
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37
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Mo L, He W, Li Z, Liang D, Qin R, Mo M, Yang C, Lin W. Recent progress in the development of DNA-based biosensors integrated with hybridization chain reaction or catalytic hairpin assembly. Front Chem 2023; 11:1134863. [PMID: 36874074 PMCID: PMC9978474 DOI: 10.3389/fchem.2023.1134863] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
As isothermal, enzyme-free signal amplification strategies, hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) possess the advantages such as high amplification efficiency, excellent biocompatibility, mild reactions, and easy operation. Therefore, they have been widely applied in DNA-based biosensors for detecting small molecules, nucleic acids, and proteins. In this review, we summarize the recent progress of DNA-based sensors employing typical and advanced HCR and CHA strategies, including branched HCR or CHA, localized HCR or CHA, and cascaded reactions. In addition, the bottlenecks of implementing HCR and CHA in biosensing applications are discussed, such as high background signals, lower amplification efficiency than enzyme-assisted techniques, slow kinetics, poor stability, and internalization of DNA probes in cellular applications.
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Affiliation(s)
- Liuting Mo
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Wanqi He
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Ziyi Li
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Danlian Liang
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Runhong Qin
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Mingxiu Mo
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Chan Yang
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Weiying Lin
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
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38
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Sterling S, Ke Y. Unraveling mechanotransduction in T cells with DNA nanotechnology. TRENDS IN CHEMISTRY 2023. [DOI: 10.1016/j.trechm.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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39
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Yan A, Sun L, Li D. Single-Molecule Imaging of Enzymatic Reactions on DNA Origami. Methods Mol Biol 2023; 2639:131-145. [PMID: 37166715 DOI: 10.1007/978-1-0716-3028-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The interaction between enzymes is very important for understanding of enzyme functions and shed light on enzymatic reaction mechanisms. With the development of DNA nanotechnology, DNA origami has become a powerful tool for analyzing the dynamic behavior of enzyme molecules. In this protocol, a method for imaging and analysis of single-molecule cascade enzyme reactions on DNA origami raft by total internal reflection fluorescence microscopy (TIRFM) is described. Through trajectory analysis and calculation, the diffusion of downstream enzymes in enzymatic reaction and chemotaxis of enzymatic reactions were elucidated at the single molecular level.
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Affiliation(s)
- An Yan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Lele Sun
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Di Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
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40
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Fàbrega C, Clua A, Eritja R, Aviñó A. Oligonucleotides Carrying Nucleoside Antimetabolites as Potential Prodrugs. Curr Med Chem 2023; 30:1304-1319. [PMID: 34844535 DOI: 10.2174/0929867328666211129124039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleoside and nucleobase antimetabolites are an important class of chemotherapeutic agents for the treatment of cancer as well as other diseases. INTRODUCTION In order to avoid undesirable side effects, several prodrug strategies have been developed. In the present review, we describe a relatively unknown strategy that consists of using oligonucleotides modified with nucleoside antimetabolites as prodrugs. METHODS The active nucleotides are generated by enzymatic degradation once incorporated into cells. This strategy has attracted large interest and is widely utilized at present due to the continuous developments made in therapeutic oligonucleotides and the recent advances in nanomaterials and nanomedicine. RESULTS A large research effort was made mainly in the improvement of the antiproliferative properties of nucleoside homopolymers, but recently, chemically modified aptamers, antisense oligonucleotides and/or siRNA carrying antiproliferative nucleotides have demonstrated a great potential due to the synergetic effect of both therapeutic entities. In addition, DNA nanostructures with interesting properties have been built to combine antimetabolites and enhancers of cellular uptake in the same scaffold. Finally, protein nanoparticles functionalized with receptor-binders and antiproliferative oligomers represent a new avenue for a more effective treatment in cancer therapy. CONCLUSION It is expected that oligonucleotides carrying nucleoside antimetabolites will be considered as potential drugs in the near future for biomedical applications.
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Affiliation(s)
- Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Clua
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
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41
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Cho KJ, Cho YE, Kim J. Locoregional Lymphatic Delivery Systems Using Nanoparticles and Hydrogels for Anticancer Immunotherapy. Pharmaceutics 2022; 14:2752. [PMID: 36559246 PMCID: PMC9788085 DOI: 10.3390/pharmaceutics14122752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
The lymphatic system has gained significant interest as a target tissue to control cancer progress, which highlights its central role in adaptive immune response. Numerous mechanistic studies have revealed the benefits of nano-sized materials in the transport of various cargos to lymph nodes, overcoming barriers associated with lymphatic physiology. The potential of sustained drug delivery systems in improving the therapeutic index of various immune modulating agents is also being actively discussed. Herein, we aim to discuss design rationales and principles of locoregional lymphatic drug delivery systems for invigorating adaptive immune response for efficient antitumor immunotherapy and provide examples of various advanced nanoparticle- and hydrogel-based formulations.
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Affiliation(s)
- Kyeong Jin Cho
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Young-Eun Cho
- Department of Food and Nutrition, Andong National University, Andong 36729, Republic of Korea
| | - Jihoon Kim
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
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42
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Zhang J, Xu Y, Chen M, Huang Y, Song T, Yang C, Yang Y, Song Y. Elucidating the Effect of Nanoscale Receptor-Binding Domain Organization on SARS-CoV-2 Infection and Immunity Activation with DNA Origami. J Am Chem Soc 2022; 144:21295-21303. [DOI: 10.1021/jacs.2c09229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yunyun Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mingying Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Ting Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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43
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Majikes JM, Liddle JA. Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology. NANOSCALE 2022; 14:15586-15595. [PMID: 36268635 PMCID: PMC10949957 DOI: 10.1039/d2nr04040a] [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] [Indexed: 06/16/2023]
Abstract
Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications. For the last 20 years, it has been suggested that NAN might be an effective replacement for parts of the semiconductor lithography or protein engineering workflows. However, in that time, these incumbent technologies have made significant advances, and our understanding of NAN's strengths and weaknesses has progressed, suggesting that the greatest opportunities in fact lie elsewhere. Given the commitment of resources necessary to bring new technologies to the market and the desire to use those resources as wisely as possible, we conduct a critical examination of where NAN may benefit from, and provide benefit to, adjacent technologies and compete least with market incumbents. While the accuracy of our conclusions may be limited by our ability to extrapolate from the current state of NAN to its future commercial success, we conclude that the next promising direction is to create a bridge between biology and semiconductor technology. We also hope to stimulate a robust conversation around this technology's capabilities with the goal of building consensus on those research and development efforts that would advance NAN to the greatest effect in real-world applications.
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Affiliation(s)
- Jacob M Majikes
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
| | - J Alexander Liddle
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
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44
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Borum RM, Lin AE, Dong X, Kai M, Chen Y. DNA Origami Disguises Herpes Simplex Virus 1 Particles and Controls Their Virulence. Molecules 2022; 27:7162. [PMID: 36363990 PMCID: PMC9656247 DOI: 10.3390/molecules27217162] [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: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 01/25/2023] Open
Abstract
DNA nanostructures are well-established vectors for packaging diversified payloads for targeted cellular delivery. Here, DNA origami rectangular sheets were combined with Herpes Simplex Virus 1 (HSV1) capsids to demonstrate surface coverage of the particle via electrostatic interactions. The optimized origami:HSV1 molar ratios led to characteristic packaging geometries ranging from dispersed "HSV1 pockets" to agglomerated "HSV1 sleeves". "Pockets" were disguised from cells in HeLa and B16F10 cells and were 44.2% less infective than naked HSV1 particles. However, the pockets were 117% more infective than naked HSV1 particles when the origami sheets were coated with folic acid. We observed infectivity from naked origami, but they are 99.1% less infective with respect to HSV1 and 99.6% less infective with respect to the pocket complexes. This work suggests that DNA origami can selectively modulate virus infectivity.
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Affiliation(s)
- Raina M. Borum
- Department of NanoEngineering, University of California, San Diego, CA 92093, USA
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45
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Zhao M, Wang R, Yang K, Jiang Y, Peng Y, Li Y, Zhang Z, Ding J, Shi S. Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharm Sin B 2022; 13:916-941. [PMID: 36970219 PMCID: PMC10031267 DOI: 10.1016/j.apsb.2022.10.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.
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Affiliation(s)
- Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Rujing Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kunmeng Yang
- The First Norman Bethune College of Clinical Medicine, Jilin University, Changchun 130061, China
| | - Yuhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
- Corresponding authors.
| | - Yachen Peng
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yuke Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Corresponding authors.
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Corresponding authors.
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46
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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48
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Dong J, O'Hagan MP, Willner I. Switchable and dynamic G-quadruplexes and their applications. Chem Soc Rev 2022; 51:7631-7661. [PMID: 35975685 DOI: 10.1039/d2cs00317a] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO2 nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.
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Affiliation(s)
- Jiantong Dong
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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49
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Hao Y, Li M, Zhang Q, Shi J, Li J, Li Q, Fan C, Wang F. DNA Origami‐Based Single‐Molecule CRISPR Machines for Spatially Resolved Searching. Angew Chem Int Ed Engl 2022; 61:e202205460. [DOI: 10.1002/anie.202205460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Yaya Hao
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Zhang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiye Shi
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Jiang Li
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- The Interdisciplinary Research Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
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50
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
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