1
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Jeong J, An SY, Hu X, Zhao Y, Yin R, Szczepaniak G, Murata H, Das SR, Matyjaszewski K. Biomass RNA for the Controlled Synthesis of Degradable Networks by Radical Polymerization. ACS NANO 2023; 17:21912-21922. [PMID: 37851525 PMCID: PMC10655241 DOI: 10.1021/acsnano.3c08244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
Nucleic acids extracted from biomass have emerged as sustainable and environmentally friendly building blocks for the fabrication of multifunctional materials. Until recently, the fabrication of biomass nucleic acid-based structures has been facilitated through simple crosslinking of biomass nucleic acids, which limits the possibility of material properties engineering. This study presents an approach to convert biomass RNA into an acrylic crosslinker through acyl imidazole chemistry. The number of acrylic moieties on RNA was engineered by varying the acylation conditions. The resulting RNA crosslinker can undergo radical copolymerization with various acrylic monomers, thereby offering a versatile route for creating materials with tunable properties (e.g., stiffness and hydrophobic characteristics). Further, reversible-deactivation radical polymerization methods, such as atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT), were also explored as additional approaches to engineer the hydrogel properties. The study also demonstrated the metallization of the biomass RNA-based material, thereby offering potential applications in enhancing electrical conductivity. Overall, this research expands the opportunities in biomass-based biomaterial fabrication, which allows tailored properties for diverse applications.
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Affiliation(s)
- Jaepil Jeong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - So Young An
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaolei Hu
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yuqi Zhao
- Department
of Materials Science & Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rongguan Yin
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Grzegorz Szczepaniak
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- University
of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland
| | - Hironobu Murata
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Subha R. Das
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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2
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Hou Y, Chen R, Wang Z, Lu R, Wang Y, Ren S, Li S, Wang Y, Han T, Yang S, Zhou H, Gao Z. Bio-barcode assay: A useful technology for ultrasensitive and logic-controlled specific detection in food safety: A review. Anal Chim Acta 2023; 1267:341351. [PMID: 37257972 DOI: 10.1016/j.aca.2023.341351] [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: 10/14/2022] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Food safety is one of the greatest public health challenges. Developing ultrasensitive detection methods for analytes at ultra-trace levels is, therefore, essential. In recent years, the bio-barcode assay (BCA) has emerged as an effective ultrasensitive detection strategy that is based on the indirect amplification of various DNA probes. This review systematically summarizes the progress of fluorescence, PCR, and colorimetry-based BCA methods for the detection of various contaminants, including pathogenic bacteria, toxins, pesticides, antibiotics, and other chemical substances in food in over 120 research papers. Current challenges, including long experimental times and strict storage conditions, and the prospects for the application of BCA in biomedicine and environmental analyses, have also been discussed herein.
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Affiliation(s)
- Yue Hou
- The Education Ministry Key Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Normal University, Shanghai, 200234, People's Republic of China; Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Ruipeng Chen
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Zhiguang Wang
- The Education Ministry Key Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Normal University, Shanghai, 200234, People's Republic of China; Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Ran Lu
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Yonghui Wang
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Shuyue Ren
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Shuang Li
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Yu Wang
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Tie Han
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Shiping Yang
- The Education Ministry Key Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Normal University, Shanghai, 200234, People's Republic of China.
| | - Huanying Zhou
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China.
| | - Zhixian Gao
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China.
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3
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Sun L, Shen F, Qu Y, Liu Z. Functional DNA as a Molecular Tool in Regulating Immunoreceptor-Ligand Interactions. JACS AU 2023; 3:1820-1834. [PMID: 37502159 PMCID: PMC10369416 DOI: 10.1021/jacsau.3c00291] [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: 06/07/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
During immune responses, activating ligands would trigger dynamic spatiotemporal organization of immunoreceptors at the cell interface, governing the fate and effector functions of immune cells. To understand the biophysical mechanisms of immunoreceptor signaling, diverse tools, including DNA technologies, have been developed to manipulate receptor-ligand interactions during the immune activation process. With great capability in the controllable assembly of biomolecules, functional DNA-based precise arrangement of immune molecules at cell interfaces has provided a powerful means in revealing the principles of immunoreceptor triggering, even at the single-molecule level. In addition, precisely regulating immunoreceptor-ligand interactions with functional DNA has been applied in immunotherapies of major diseases. This Perspective will focus on the recent advances in exploring immunoreceptor signaling with functional DNA as the molecular tool as well as the applications of functional DNA mediated regulation of immunoreceptor activation. We also outline the challenges and opportunities of applying functional DNA in immune modulation and immunotherapy.
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Affiliation(s)
- Lele Sun
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Fengyun Shen
- School
of Chemistry and Chemical Engineering, Shanghai
Jiao Tong University, Shanghai 201240, China
| | - Yanfei Qu
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Zhuang Liu
- Institute
of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Lab
Carbon Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
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4
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Ding F, Zhang S, Chen Q, Feng H, Ge Z, Zuo X, Fan C, Li Q, Xia Q. Immunomodulation with Nucleic Acid Nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206228. [PMID: 36599642 DOI: 10.1002/smll.202206228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
The precise regulation of interactions of specific immunological components is crucial for controllable immunomodulation, yet it remains a great challenge. With the assistance of advanced computer design, programmable nucleic acid nanotechnology enables the customization of synthetic nucleic acid nanodevices with unprecedented geometrical and functional precision, which have shown promising potential for precise immunoengineering. Notably, the inherently immunologic functions of nucleic acids endow these nucleic acid-based assemblies with innate advantages in immunomodulatory engagement. In this review, the roles of nucleic acids in innate immunity are discussed, focusing on the definition, immunologic modularity, and enhanced bioavailability of structural nucleic acid nanodevices. In light of this, molecular programming and precise organization of functional modules with nucleic acid nanodevices for immunomodulation are emphatically reviewed. At last, the present challenges and future perspectives of nucleic acid nanodevices for immunomodulation are discussed.
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Affiliation(s)
- Fei Ding
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Shuangye 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, P. R. China
| | - Qian Chen
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Hao Feng
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xiaolei Zuo
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. 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, P. R. 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, P. R. China
- WLA Laboratories, World Laureates Association, Shanghai, 201203, P. R. China
| | - Qiang Xia
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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5
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Ling J, Liu D, Zhang J, Zhu L, Wan S, Yang C, Song Y. Thermodynamic and Kinetic Modulation of Microfluidic Interfaces by DNA Nanoassembly Mediated Merit-Complementary Heteromultivalency. ACS NANO 2022; 16:20915-20921. [PMID: 36416763 DOI: 10.1021/acsnano.2c08507] [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: 06/16/2023]
Abstract
The multivalent effect is often used to engineer microfluidic affinity interfaces to improve the target separation efficiency. Currently, no design rules exist for thermodynamic and kinetic tuning of properly joining multiple ligands. Herein, we developed a thermodynamic and kinetic modulating strategy of the microfluidic affinity interface via a merit-complementary-heteromultivalent aptamers functionalized DNA nanoassembly. Our strategy is built on the two types of identified aptamers that bind to distinct sites of EpCAM. The aptamer binding of one type is more rapid but less tight, while the other is opposite. By assembling the two types of aptamers together with a tetrahedral DNA framework, we fully exploited these aptamers' merits for tight and rapid recognition of EpCAM, leading to target cell capture with high efficiency and throughput. Our strategy provides a perspective on engineering multivalent recognition molecules through thermodynamic and kinetic tuning.
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Affiliation(s)
- Jiajun Ling
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen361005, China
| | - Dan Liu
- School of Biomedical Sciences, Huaqiao University, Fujian361000, China
| | - Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen361005, China
| | - Lin Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen361005, China
| | - Shuang Wan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen361005, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen361005, China
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6
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Zhang J, Song C, Wang L. DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications. Phys Chem Chem Phys 2022; 24:23959-23979. [PMID: 36168789 DOI: 10.1039/d2cp02100e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.
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Affiliation(s)
- Jingjing Zhang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Chunyuan Song
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Lianhui Wang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
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7
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McCarte B, Yeung OT, Speakman AJ, Elfick A, Dunn KE. Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures. Biochem Biophys Rep 2022; 31:101293. [PMID: 35677630 PMCID: PMC9167695 DOI: 10.1016/j.bbrep.2022.101293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/21/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
Non-canonical forms of DNA are attracting increasing interest for applications in nanotechnology. It is frequently convenient to characterize DNA molecules using a label-free approach such as ultraviolet absorption spectroscopy. In this paper we present the results of our investigation into the use of this technique to probe the folding of quadruplex and triplex nanoswitches. We confirmed that four G-quartets were necessary for folding at sub-mM concentrations of potassium and found that the wrong choice of sequence for the linker between G-tracts could dramatically disrupt folding, presumably due to the presence of kinetic traps in the folding landscape. In the case of the triplex nanoswitch we examined, we found that the UV spectrum showed a small change in absorbance when a triplex was formed. We anticipate that our results will be of interest to researchers seeking to design DNA nanoswitches based on quadruplexes and triplexes. Ultraviolet absorption spectroscopy can probe non-canonical DNA structures. Absorbance at 295 nm tends to increase as G-quadruplexes form. Four G-quartets are needed to form a quadruplex with less than 1 mM potassium. Formation of DNA triplexes can also yield a small change in UV spectra. UV absorption is a cheap label-free method for studying DNA nanoswitches.
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8
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Wang Y, Wang Z, Wu X, Liu S, Liu F, Jiang Q, Ding B. DNA Nanodevices: from Mechanical Motions to Biomedical Applications. Curr Top Med Chem 2021; 22:640-651. [PMID: 34749612 DOI: 10.2174/1568026621666211105100240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022]
Abstract
Inspired by molecular machines in nature, artificial nanodevices have been designed to realize various biomedical functions. Self-assembled deoxyribonucleic acid (DNA) nanostructures that feature designed geometries, excellent spatial accuracy, nanoscale addressability and marked biocompatibility provide an attractive candidate for constructing dynamic nanodevices with biomarker-targeting and stimuli-responsiveness for biomedical applications. Here, a summary of typical construction strategies of DNA nanodevices and their operating mechanisms are presented. We also introduced recent advances in employing DNA nanodevices as platforms for biosensing and intelligent drug delivery. Finally, the broad prospects and main challenges of the DNA nanodevices in biomedical applications are discussed.
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Affiliation(s)
- Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Zhaoran Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Shaoli Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Fengsong Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
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10
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Chen S, Xing L, Zhang D, Monferrer A, Hermann T. Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid. Nucleic Acids Res 2021; 49:10098-10105. [PMID: 34500473 PMCID: PMC8464029 DOI: 10.1093/nar/gkab797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/06/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022] Open
Abstract
Design and preparation of layered composite materials alternating between nucleic acids and proteins has been elusive due to limitations in occurrence and geometry of interaction sites in natural biomolecules. We report the design and kinetically controlled stepwise synthesis of a nano-sandwich composite by programmed noncovalent association of protein, DNA and RNA modules. A homo-tetramer protein core was introduced to control the self-assembly and precise positioning of two RNA–DNA hybrid nanotriangles in a co-parallel sandwich arrangement. Kinetically favored self-assembly of the circularly closed nanostructures at the protein was driven by the intrinsic fast folding ability of RNA corner modules which were added to precursor complex of DNA bound to the protein. The 3D architecture of this first synthetic protein–RNA–DNA complex was confirmed by fluorescence labeling and cryo-electron microscopy studies. The synthesis strategy for the nano-sandwich composite provides a general blueprint for controlled noncovalent assembly of complex supramolecular architectures from protein, DNA and RNA components, which expand the design repertoire for bottom-up preparation of layered biomaterials.
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Affiliation(s)
- Shi Chen
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Li Xing
- Irvine Materials Research Institute, University of California, Irvine, CA 92697, USA
| | - Douglas Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Alba Monferrer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Thomas Hermann
- To whom correspondence should be addressed. Tel: +1 858 534 4467; Fax: +1 858 534 0202;
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11
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Chai H, Cheng W, Jin D, Miao P. Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing. ACS APPLIED MATERIALS & INTERFACES 2021; 13:38931-38946. [PMID: 34374513 DOI: 10.1021/acsami.1c09000] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.
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Affiliation(s)
- Hua Chai
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Wenbo Cheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Dayong Jin
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia
- UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
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12
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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13
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Jiang C, Zhang Y, Wang F, Liu H. Toward Smart Information Processing with Synthetic DNA Molecules. Macromol Rapid Commun 2021; 42:e2100084. [PMID: 33864315 DOI: 10.1002/marc.202100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Indexed: 11/07/2022]
Abstract
DNA, a biological macromolecule, is a naturally evolved information material. From the structural point of view, an individual DNA strand can be considered as a chain of data with its bases working as single units. For decades, due to the high biochemical stability, large information storage capacity, and high recognition specificity, DNA has been recognized as an attractive material for information processing. Especially, the chemical synthesis strategies and DNA sequencing techniques have been rapidly developed recently, further enabling encoding information with synthetic DNA molecules. Herein, recent progresses are summarized on information processing based on synthetic DNA molecules from three aspects including information storage, computation, and encryption, and proposed the challenges and future development directions.
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Affiliation(s)
- Chu Jiang
- School of Chemical Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Shanghai Research Institute for Intelligent Autonomous Systems, Tongji University, Shanghai, 200092, China
| | - Yinan 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
- Center for Molecular Design and Biomimetics, School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - 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
| | - Huajie Liu
- School of Chemical Science and Engineering, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Shanghai Research Institute for Intelligent Autonomous Systems, Tongji University, Shanghai, 200092, China
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14
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Ariga K. Nanoarchitectonics Revolution and Evolution: From Small Science to Big Technology. SMALL SCIENCE 2020. [DOI: 10.1002/smsc.202000032] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA) National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba 305-0044 Japan
- Department of Advanced Materials Science Graduate School of Frontier Sciences The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8561 Japan
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15
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Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020; 64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fujian Huang
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Yanyi Huang
- College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 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
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin, 300071 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Libing Liu
- Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chunhua Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing, 100084 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Shu Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for 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, 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for 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, 361005 China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Huanghao Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Weihong Tan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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16
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Zhang B, Martens K, Kneer L, Funck T, Nguyen L, Berger R, Dass M, Kempter S, Schmidtke J, Liedl T, Kitzerow HS. DNA Origami Nano-Sheets and Nano-Rods Alter the Orientational Order in a Lyotropic Chromonic Liquid Crystal. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1695. [PMID: 32872176 PMCID: PMC7560128 DOI: 10.3390/nano10091695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/28/2022]
Abstract
Rod-like and sheet-like nano-particles made of desoxyribonucleic acid (DNA) fabricated by the DNA origami method (base sequence-controlled self-organized folding of DNA) are dispersed in a lyotropic chromonic liquid crystal made of an aqueous solution of disodium cromoglycate. The respective liquid crystalline nanodispersions are doped with a dichroic fluorescent dye and their orientational order parameter is studied by means of polarized fluorescence spectroscopy. The presence of the nano-particles is found to slightly reduce the orientational order parameter of the nematic mesophase. Nano-rods with a large length/width ratio tend to preserve the orientational order, while more compact stiff nano-rods and especially nano-sheets reduce the order parameter to a larger extent. In spite of the difference between the sizes of the DNA nano-particles and the rod-like columnar aggregates forming the liquid crystal, a similarity between the shapes of the former and the latter seems to be better compatible with the orientational order of the liquid crystal.
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Affiliation(s)
- Bingru Zhang
- Faculty of Science, Department of Chemistry, University of Paderborn, Warburger Straße 100, 33098 Paderborn, Germany; (B.Z.); (J.S.)
| | - Kevin Martens
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Luisa Kneer
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Timon Funck
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Linh Nguyen
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Ricarda Berger
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Mihir Dass
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Susanne Kempter
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Jürgen Schmidtke
- Faculty of Science, Department of Chemistry, University of Paderborn, Warburger Straße 100, 33098 Paderborn, Germany; (B.Z.); (J.S.)
| | - Tim Liedl
- Faculty of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany; (K.M.); (L.K.); (T.F.); (L.N.); (R.B.); (M.D.); (S.K.); (T.L.)
| | - Heinz-S. Kitzerow
- Faculty of Science, Department of Chemistry, University of Paderborn, Warburger Straße 100, 33098 Paderborn, Germany; (B.Z.); (J.S.)
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17
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Mao X, Liu M, Yan L, Deng M, Li F, Li M, Wang F, Li J, Wang L, Tian Y, Fan C, Zuo X. Programming Biomimetically Confined Aptamers with DNA Frameworks. ACS NANO 2020; 14:8776-8783. [PMID: 32484652 DOI: 10.1021/acsnano.0c03362] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Active sites of proteins are generally encapsulated within three-dimensional peptide scaffolds that provide the molecular-scale confinement microenvironment. Nevertheless, the ability to tune thermodynamic stability in biomimetic molecular confinement relies on the macromolecular crowding effect of lack of stoichiometry and reconfigurability. Here, we report a framework nucleic acid (FNA)-based strategy to increase thermodynamic stability of aptamers. We demonstrate that the molecular-scale confinement increases the thermodynamic stability of aptamers via facilitated folding kinetics, which is confirmed by the single-molecule FRET (smFRET). Unfavorable conformations of aptamers are restricted as revealed by the Monte Carlo simulation. The binding affinity of the DNA framework-confined aptamer is improved by ∼3-fold. With a similar strategy we improve the catalytic activity of hemin-binding aptamer. Our approach thus shows high potential for designing protein-mimicking DNA nanostructures with enhanced binding affinity and catalytic activity for biosensing and biomedical engineering.
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Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Lei Yan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengying Deng
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fei Wang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai 201499, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University,, Shanghai 200240, 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
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University,, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University,, Shanghai 200240, China
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18
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Peng T, Li X, Li K, Nie Z, Tan W. DNA-Modulated Plasmon Resonance: Methods and Optical Applications. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14741-14760. [PMID: 32154704 DOI: 10.1021/acsami.9b23608] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The near-field effects in the vicinity of metallic nanoparticle surfaces, as induced by electromagnetic radiation with specific wavelength, give rise to a variety of novel optical properties and attractive applications because of surface plasmons, which are the coherent oscillations of conduction electrons on a metal surface. The interdisciplinary field of plasmonics has witnessed vigorous growth, promoting research on the modulation of plasmon resonance by constructing advanced plasmonic nanoarchitectures with controllable size, morphology, or interparticle coupling. Among diversified tools, deoxyribonucleic nucleic acid (DNA) possesses prominent superiority as a result of its designability, programmability, addressability, and ease of nanomaterial modification. In this review, we focus on the methods and optical applications of plasmon resonance modulation accomplished by DNA nanotechnology. Recent developments in the construction of DNA-mediated plasmonic nanoarchitecture and key ongoing research directions utilizing unique optical features are highlighted. Obstacles and challenges in this field are pointed out, followed by preliminary suggestions on some areas of opportunity that deserve attention.
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Affiliation(s)
- Tianhuan Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
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