1
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Qu Y, Shen F, Peng H, Chen G, Wang L, Sun L. Dynamic Interface-Assisted Rapid Self-Assembly of DNA Origami-Framed Anisotropic Nanoparticles. JACS AU 2024; 4:903-907. [PMID: 38559741 PMCID: PMC10976600 DOI: 10.1021/jacsau.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The ordered arrangement of nanoparticles can generate unique physicochemical properties, rendering it a pivotal direction in the field of nanotechnology. DNA-based chemical encoding has emerged as an unparalleled strategy for orchestrating precise and controlled nanoparticle assemblies. Nonetheless, it is often time-consuming and has limited assembly efficiency. In this study, we developed a strategy for the rapid and ordered assembly of DNA origami-framed nanoparticles assisted by dynamic interfaces. By assembling Au nanoparticles (AuNPs) onto DNA origami with different sticky ends in various directions, we endowed them with anisotropic specific affinities. After assembling DNA origami-framed AuNPs onto supported lipid bilayers with freely diffusing single-stranded DNA via DNA hybridization, we found that DNA origami-framed AuNPs could form larger ordered assemblies than those in 3D solution within equivalent time frames. Furthermore, we also achieved rapid and ordered assembly of liposome nanoparticles by employing the aforementioned strategy. Our work provides a novel avenue for efficient and rapid assembly of nanoparticles across two-dimensional interfaces, which is expected to promote the application of ordered nanoparticle assemblies in sensor and biomimetic system construction.
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Affiliation(s)
- Yanfei Qu
- School
of Life Science, Shanghai University, Shanghai 200444, China
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Fengyun Shen
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Hongzhen Peng
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Guifang Chen
- School
of Life Science, Shanghai University, Shanghai 200444, China
| | - Lihua Wang
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Lele Sun
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
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2
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Ding L, Chen X, Ma W, Li J, Liu X, Fan C, Yao G. DNA-mediated regioselective encoding of colloids for programmable self-assembly. Chem Soc Rev 2023; 52:5684-5705. [PMID: 37522252 DOI: 10.1039/d2cs00845a] [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: 08/01/2023]
Abstract
How far we can push chemical self-assembly is one of the most important scientific questions of the century. Colloidal self-assembly is a bottom-up technique for the rational design of functional materials with desirable collective properties. Due to the programmability of DNA base pairing, surface modification of colloidal particles with DNA has become fundamental for programmable material self-assembly. However, there remains an ever-lasting demand for surface regioselective encoding to realize assemblies that require specific, directional, and orthogonal interactions. Recent advances in surface chemistry have enabled regioselective control over the formation of DNA bonds on the particle surface. In particular, the structural DNA nanotechnology provides a simple yet powerful design strategy with unique regioselective addressability, bringing the complexity of colloidal self-assembly to an unprecedented level. In this review, we summarize the state-of-art advances in DNA-mediated regioselective surface encoding of colloids, with a focus on how the regioselective encoding is introduced and how the regioselective DNA recognition plays a crucial role in the self-assembly of colloidal structures. This review highlights the advantages of DNA-based regioselective modification in improving the complexity of colloidal assembly, and outlines the challenges and opportunities for the construction of more complex architectures with tailored functionalities.
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Affiliation(s)
- Longjiang Ding
- 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.
| | - Xiaoliang Chen
- 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.
| | - Wenhe Ma
- 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.
| | - Jiang Li
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Xiaoguo Liu
- 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.
| | - Guangbao Yao
- 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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3
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Yang S, Wang Y, Wang Q, Li F, Ling D. DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:340-355. [PMID: 37501793 PMCID: PMC10369495 DOI: 10.1021/cbmi.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/07/2023] [Indexed: 07/29/2023]
Abstract
DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.
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Affiliation(s)
- Shengfei Yang
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuqi Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Qiyue Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Fangyuan Li
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
| | - Daishun Ling
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
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4
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Abstract
DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to physically detectable signals, various nanomaterials have been extensively exploited to take advantage of their optical and surface properties. A popular sensing scheme is through the adsorption of a fluorescently-labeled DNA probe, where detection is achieved by target-induced probe desorption and fluorescence recovery. Another method is to use DNA to protect the colloidal stability of nanomaterials, where subsequent target binding can decrease the protection ability and induce aggregation; this method has mainly been used for gold nanoparticles. This Perspective summarizes some of our work in examining the sensing mechanisms, and we articulate the importance of the understanding of DNA/surface and target/surface interactions for the development of practical DNA-based biosensors.
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Affiliation(s)
- Stefen Stangherlin
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, ON, N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, ON, N2L 3G1, Canada.
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5
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Li K, Liu Y, Lou B, Tan Y, Chen L, Liu Z. DNA-Guided Metallization of Nanomaterials and Their Biomedical Applications. Molecules 2023; 28:molecules28093922. [PMID: 37175332 PMCID: PMC10180097 DOI: 10.3390/molecules28093922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Precise control of the structure of metallic nanomaterials is critical for the advancement of nanobiotechnology. As DNA (deoxyribonucleic acid) can readily modify various moieties, such as sulfhydryl, carboxyl, and amino groups, using DNA as a directing ligand to modulate the morphology of nanomaterials is a promising strategy. In this review, we focus on the use of DNA as a template to control the morphology of metallic nanoparticles and their biomedical applications, discuss the use of DNA for the metallization of gold and silver, explore the factors that influence the process, and outline its biomedical applications. This review aims to provide valuable insights into the DNA-guided growth of nanomaterials. The challenges and future directions are also discussed.
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Affiliation(s)
- Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Beibei Lou
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Liwei Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
- Molecular Imaging Research Center of Central South University, Changsha 410008, China
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6
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Guan X, Li Z, Geng X, Lei Z, Karakoti A, Wu T, Kumar P, Yi J, Vinu A. Emerging Trends of Carbon-Based Quantum Dots: Nanoarchitectonics and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207181. [PMID: 36693792 DOI: 10.1002/smll.202207181] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Carbon-based quantum dots (QDs) have emerged as a fascinating class of advanced materials with a unique combination of optoelectronic, biocompatible, and catalytic characteristics, apt for a plethora of applications ranging from electronic to photoelectrochemical devices. Recent research works have established carbon-based QDs for those frontline applications through improvements in materials design, processing, and device stability. This review broadly presents the recent progress in the synthesis of carbon-based QDs, including carbon QDs, graphene QDs, graphitic carbon nitride QDs and their heterostructures, as well as their salient applications. The synthesis methods of carbon-based QDs are first introduced, followed by an extensive discussion of the dependence of the device performance on the intrinsic properties and nanostructures of carbon-based QDs, aiming to present the general strategies for device designing with optimal performance. Furthermore, diverse applications of carbon-based QDs are presented, with an emphasis on the relationship between band alignment, charge transfer, and performance improvement. Among the applications discussed in this review, much focus is given to photo and electrocatalytic, energy storage and conversion, and bioapplications, which pose a grand challenge for rational materials and device designs. Finally, a summary is presented, and existing challenges and future directions are elaborated.
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Affiliation(s)
- Xinwei Guan
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
- School of Materials Science and Engineering, University of New South Wales (UNSW), Sydney, NSW, 2052, Australia
| | - Zhixuan Li
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Xun Geng
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Zhihao Lei
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Ajay Karakoti
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Tom Wu
- School of Materials Science and Engineering, University of New South Wales (UNSW), Sydney, NSW, 2052, Australia
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, 999077, P. R. China
| | - Prashant Kumar
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Jiabao Yi
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Ajayan Vinu
- Global Innovative Centre for Advanced Nanomaterials, School of Engineering, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, 2308, Australia
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7
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Zuo L, Ren K, Guo X, Pokhrel P, Pokhrel B, Hossain MA, Chen ZX, Mao H, Shen H. Amalgamation of DNAzymes and Nanozymes in a Coronazyme. J Am Chem Soc 2023; 145:5750-5758. [PMID: 36795472 PMCID: PMC10325850 DOI: 10.1021/jacs.2c12367] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Artificial enzymes such as nanozymes and DNAzymes are economical and stable alternatives to natural enzymes. By coating Au nanoparticles (AuNPs) with a DNA corona (AuNP@DNA), we amalgamated nanozymes and DNAzymes into a new artificial enzyme with catalytic efficiency 5 times higher than AuNP nanozymes, 10 times higher than other nanozymes, and significantly greater than most of the DNAzymes on the same oxidation reaction. The AuNP@DNA demonstrates excellent specificity as its reactivity on a reduction reaction does not change with respect to pristine AuNP. Single-molecule fluorescence and force spectroscopies and density functional theory (DFT) simulations indicate a long-range oxidation reaction initiated by radical production on the AuNP surface, followed by radical transport to the DNA corona, where the binding and turnover of substrates take place. The AuNP@DNA is named coronazyme because of its natural enzyme mimicking capability through the well-orchestrated structures and synergetic functions. By incorporating different nanocores and corona materials beyond DNAs, we anticipate that the coronazymes represent generic enzyme mimics to carry out versatile reactions in harsh environments.
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Affiliation(s)
- Li Zuo
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Kehao Ren
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Xianming Guo
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Bishal Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | | | - Zhao-Xu Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Hao Shen
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
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8
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Ding Y, Huang PJJ, Zandieh M, Wang J, Liu J. Gold Nanoparticles Synthesized Using Various Reducing Agents and the Effect of Aging for DNA Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:256-264. [PMID: 36577094 DOI: 10.1021/acs.langmuir.2c02458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Gold nanoparticles (AuNPs) are one of the most commonly used reagents in colloidal science and biosensor technology. In this work, we first compared AuNPs prepared using four different reducing agents including citrate, glucose, ascorbate, and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES). At the same absorbance at the surface plasmon peak of 520-530 nm, citrate-AuNPs and glucose-AuNPs adsorbed more DNA and achieved higher affinity to the adsorbed DNA. In addition, citrate-AuNPs had better sensitivity than glucose-AuNPs for label-free DNA detection. Then, using citrate-AuNPs, the effect of aging was studied by incubation of the AuNPs at 22 °C (room temperature) and at 4 °C for up to 6 months. During aging, the colloidal stability and DNA adsorption efficiency gradually decreased. In addition, the DNA sensing sensitivity using a label-free method also dropped around 4-fold after 6 months. Heating at boiling temperature of the aged citrate-AuNPs could not rejuvenate the sensing performance. This study shows that while citrate-AuNPs are initially better than the other three AuNPs in their colloid properties and sensing properties, this edge in performance might gradually decrease due to constantly changing surface properties caused from the aging effect.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Mohamad Zandieh
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Jinghan Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
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9
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Song T, Wang X, Yao D, Liang H, Lu Y. Identifying and Differentiating Topological G-Quadruplex Structures with DNA-Encoded Plasmonic Gold Nanoparticles. Angew Chem Int Ed Engl 2022; 61:e202204201. [PMID: 35894268 PMCID: PMC9489634 DOI: 10.1002/anie.202204201] [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: 03/21/2022] [Indexed: 11/10/2022]
Abstract
DNA G-quadruplexes (G4s) have been identified as critical elements in modulating genomic functions and many other biological processes. Their functions are highly dependent on the primary nucleotides and secondary folding structures. Therefore, to understand their functions, methods to identify and differentiate structures of G4 with speed and accuracy are required but limited. In this report, we have applied a synthetic G4 DNA-encoded nanoparticle approach to identify and differentiate G4 DNA molecules with different topologies and nucleotide residues. We found that the resulting plasmonic properties of the gold nanoparticles, monitored by UV/Vis spectroscopy, are quite sensitive to different G4 structures, including stacking layers, loop sequences, capping bases on G4s, and topological structures. Through these systematic investigations, we demonstrate that this G4-encoded gold nanoparticle approach can be used to profile the G4 structures and distinguish G4s from human telomeres. Such a method may have wide applications in G4 research.
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Affiliation(s)
- Tingjie Song
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiaojing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Dongbao Yao
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Haojun Liang
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
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10
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Song T, Wang X, Yao D, Liang H, Lu Y. Identifying and Differentiating Topological G‐Quadruplex Structures with DNA‐encoded Plasmonic Gold Nanoparticles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tingjie Song
- University of Illinois at Urbana-Champaign Chemistry A429 CLSL,600 South Mathews Avenue 61801 Urbana UNITED STATES
| | - Xiaojing Wang
- University of Illinois at Urbana-Champaign Chemistry 600 South Mathews Avenue 61801 Urbana UNITED STATES
| | - Dongbao Yao
- University of Science and Technology of China Polymer Science and Engineering jinzhai Road, NO.96 230026 hefei CHINA
| | - Haojun Liang
- University of Science and Technology of China Polymer Science and Engineering jinzhai Road, NO.96 230026 hefei CHINA
| | - Yi Lu
- University of Illinois Chemistry 600 South Mathews Ave. 61801 Urbana UNITED STATES
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11
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The effectiveness of silver nanoparticles as a clean-up material for water polluted with bacteria DNA conveying antibiotics resistance genes: Effect of different molar concentrations and competing ions. OPENNANO 2022. [DOI: 10.1016/j.onano.2022.100060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Catalytic hairpin assembly assisted target-dependent DNAzyme nanosystem coupled with AgPt@Thi for the detection of lead ion. Anal Chim Acta 2022; 1205:339735. [DOI: 10.1016/j.aca.2022.339735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/19/2022]
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13
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Kong Y, Du Q, Li J, Xing H. Engineering bacterial surface interactions using DNA as a programmable material. Chem Commun (Camb) 2022; 58:3086-3100. [PMID: 35077527 DOI: 10.1039/d1cc06138k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and synthetically control the biological functions of individual cells as well as the whole community, there is growing attention on the development of chemical and biological tools that can integrate artificial functional motifs onto the bacterial surface to replace the native interactions, enabling a variety of applications in biosynthesis, environmental protection, and human health. Among all these functional motifs, DNA emerges as a powerful tool that can precisely control bacterial interactions at the bio-interface due to its programmability and biorecognition properties. Compared with conventional chemical and genetic approaches, the sequence-specific Watson-Crick interaction enables almost unlimited programmability in DNA nanostructures, realizing one base-pair spatial control and bio-responsive properties. This highlight aims to provide an overview on this emerging research topic of DNA-engineered bacterial interactions from the aspect of synthetic chemists. We start with the introduction of native bacterial surface ligands and established synthetic approaches to install artificial ligands, including direct modification, metabolic engineering, and genetic engineering. A brief overview of DNA nanotechnology, reported DNA-bacteria conjugation chemistries, and several examples of DNA-engineered bacteria are included in this highlight. The future perspectives and challenges in this field are also discussed, including the development of dynamic bacterial surface chemistry, assembly of programmable multicellular community, and realization of bacteria-based theranostic agents and synthetic microbiota as long-term goals.
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Affiliation(s)
- Yuhan Kong
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Qi Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Juan Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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14
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Zhan S, Jiang J, Zeng Z, Wang Y, Cui H. DNA-templated coinage metal nanostructures and their applications in bioanalysis and biomedicine. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Liu F, Liu X, Huang Q, Arai T. Recent Progress of Magnetically Actuated DNA Micro/Nanorobots. CYBORG AND BIONIC SYSTEMS 2022; 2022:9758460. [PMID: 36285315 PMCID: PMC9494703 DOI: 10.34133/2022/9758460] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/22/2021] [Indexed: 01/12/2023] Open
Abstract
In the past few decades, the field of DNA origami-based micro/nanotechnology has developed dramatically and spawned attention increasingly, as its high integrality, rigid structure, and excellent resistance ability to enzyme digestion. Many two-dimensional and three-dimensional DNA nanostructures coordinated with optical, chemical, or magnetic triggers have been designed and assembled, extensively used as versatile templates for molecular robots, nanosensors, and intracellular drug delivery. The magnetic field has been widely regarded as an ideal driving and operating system for micro/nanomaterials, as it does not require high-intensity lasers like light control, nor does it need to change the chemical composition similar to chemical activation. Herein, we review the recent achievements in the induction and actuation of DNA origami-based nanodevices that respond to magnetic fields. These magnetic actuation-based DNA nanodevices were regularly combined with magnetic beads or gold nanoparticles and applied to generate single-stranded scaffolds, assemble various DNA nanostructures, and purify specific DNA nanostructures. Moreover, they also produced artificial magnetism or moved regularly driven by external magnetic fields to explain deeper scientific issues.
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Affiliation(s)
- Fengyu Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoming Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiang Huang
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Tatsuo Arai
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Tokyo 182-8585, Japan
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16
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Zhao P, Li B, Li Y, Chen L, Wang H, Ye L. DNA-Templated ultrasmall bismuth sulfide nanoparticles for photoacoustic imaging of myocardial infarction. J Colloid Interface Sci 2022; 615:475-484. [PMID: 35150955 DOI: 10.1016/j.jcis.2022.01.194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 10/19/2022]
Abstract
Photoacoustic imaging (PAI) has shown great clinical potential in diagnosing various diseases due to its noninvasive, cost-effective, and real-time imaging properties but is limited by the lack of contrast agents with high sensitivity for deep tissue imaging. Here, DNA-templated ultrasmall bismuth sulfide (Bi2S3) nanoparticles (NPs) were reported as a photoacoustic (PA) probe for imaging myocardial infarction. We present a simple synthesis strategy of ultrasmall NPs via self-assembly of single-stranded DNA (ssDNA)/metal ion complexes. The in vivo imaging results showed a dramatically enhanced PA signal in the region of myocardial infarction after intravenous injection of DNA-Bi2S3 NPs in the myocardial ischaemia/reperfusion (I/R) mouse model. Further near infrared fluorescence imaging indicated that Bi2S3 NPs mainly accumulated in the infarcted area, leading to enhancement of PA signals. Moreover, such hybrid NPs possess a well-defined nanostructure, superior photobleaching resistance, excellent water dispersibility and negligible acute toxicity. These results not only demonstrate that ultrasmall DNA-Bi2S3 NPs are a potent PA probe for imaging the infarcted region but also provide a new avenue for preparing ultrasmall-sized PA probes by using ssDNA as a template.
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Affiliation(s)
- Peng Zhao
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, PR. China
| | - Bing Li
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR. China
| | - Yingxu Li
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR. China
| | - Leshan Chen
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, PR. China
| | - Hao Wang
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR. China.
| | - Ling Ye
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, PR. China
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17
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Singh H, Ahmed I, Biswas R, Mete S, Halder KK, Banerjee B, Haldar KK. Genomic DNA-mediated formation of a porous Cu 2(OH)PO 4/Co 3(PO 4) 2·8H 2O rolling pin shape bifunctional electrocatalyst for water splitting reactions. RSC Adv 2022; 12:3738-3744. [PMID: 35425395 PMCID: PMC8979272 DOI: 10.1039/d1ra09098d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/05/2022] [Indexed: 12/22/2022] Open
Abstract
Among the accessible techniques, the production of hydrogen by electrocatalytic water oxidation is the most established process, which comprises oxygen evolution reaction (OER) and hydrogen evolution reaction (HER). Here, we synthesized a genomic DNA-guided porous Cu2(OH)PO4/Co3(PO4)2·8H2O rolling pin shape composite structure in one pot. The nucleation and development of the porous rolling pin shape Cu2(OH)PO4/Co3(PO4)2·8H2O composite was controlled and stabilized by the DNA biomolecules. This porous rolling pin shape composite was explored towards electrocatalytic water oxidation for both OER and HER as a bi-functional catalyst. The as-prepared catalyst exhibited a very high OER and HER activity compared to its various counterparts in the absence of an external binder (such as Nafion). The synergistic effects between Cu and Co metals together with the porous structure of the composite greatly helped in enhancing the catalytic activity. These outcomes undoubtedly demonstrated the beneficial utilization of the genomic DNA-stabilised porous electrocatalyst for OER and HER, which has never been observed.
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Affiliation(s)
- Harjinder Singh
- Department of Chemistry, Central University of Punjab 151001-Bathinda Punjab India
| | - Imtiaz Ahmed
- Department of Chemistry, Central University of Punjab 151001-Bathinda Punjab India
| | - Rathindranath Biswas
- Department of Chemistry, Central University of Punjab 151001-Bathinda Punjab India
| | - Shouvik Mete
- Department of Chemistry, Central University of Punjab 151001-Bathinda Punjab India
| | | | - Biplab Banerjee
- Department of Chemistry, Central University of Punjab 151001-Bathinda Punjab India
| | - Krishna Kanta Haldar
- Department of Chemistry, Central University of Punjab 151001-Bathinda Punjab India
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18
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Lu C, Zhou S, Gao F, Lin J, Liu J, Zheng J. DNA-Mediated Growth of Noble Metal Nanomaterials for Biosensing Applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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19
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Li S, Zeng Z, Zhao C, Wang H, Ye X, Qing T. Nucleoside-regulated catalytic activity of copper nanoclusters and their application for mercury ion detection. NEW J CHEM 2022. [DOI: 10.1039/d1nj05525a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a novel method for the synthesis of copper nanoclusters is developed using nucleosides as templates and hydroxylamine hydrochloride as the reductant. Various nucleosides can regulate the catalytic activity of copper nanoclusters.
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Affiliation(s)
- Shiyan Li
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, Hunan Province, China
| | - Zihang Zeng
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, Hunan Province, China
| | - Congcong Zhao
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, Hunan Province, China
| | - Haoyu Wang
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, Hunan Province, China
| | - Xiaosheng Ye
- Xiangya School of Public Health, Central South University, Changsha 410078, Hunan Province, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Taiping Qing
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, Hunan Province, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
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20
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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21
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Abstract
Among transition metal nanoparticles, palladium nanoparticles (PdNPs) are recognized for their high catalytic activity in a wide range of organic transformations that are of academic and industrial importance. The increased interest in environmental issues has led to the development of various green approaches for the preparation of efficient, low-cost and environmentally sustainable Pd-nanocatalysts. Environmentally friendly solvents, non-toxic reducing reagents, biodegradable capping and stabilizing agents and energy-efficient synthetic methods are the main aspects that have been taken into account for the production of Pd nanoparticles in a green approach. This review provides an overview of the fundamental approaches used for the green synthesis of PdNPs and their catalytic application in sustainable processes as cross-coupling reactions and reductions with particular attention afforded to the recovery and reuse of the palladium nanocatalyst, from 2015 to the present.
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22
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Zhang F, Liu J. Interactions of the Cocaine and Quinine Aptamer with Gold Nanoparticles under the Dilute Biosensor and Concentrated NMR Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11939-11947. [PMID: 34591480 DOI: 10.1021/acs.langmuir.1c02239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The cocaine aptamer was later found to bind quinine with an even higher affinity. In this work, we used a fluorescently labeled aptamer named MN4 to study its adsorption by gold nanoparticles (AuNPs), and the subsequent displacement by the nonlabeled aptamer and by quinine. Without washing, 14% of the preadsorbed MN4 strands were displaced by 4000-fold excess of free MN4, whereas no displacement was observed after washing, suggesting that washing removed weakly adsorbed aptamers. In a previous paper, rapid exchange was observed with NMR by directly mixing AuNPs and concentrated MN4, and our work has unified the dilute and concentrated aptamer conditions. The difference is attributable to the conformation of the adsorbed aptamer, where dilute aptamers are adsorbed in a collapsed state with a much higher affinity to AuNPs. In addition, the preadsorbed MN4 aptamer cannot be desorbed by adding quinine, indicating that direct desorption-based fluorescent sensors cannot be made. Finally, based on the similar color responses to both the aptamer and its nonbinding mutants, the label-free colorimetric detection method cannot be directly applied for the detection of quinine. This work indicated that different experimental conditions need to be carefully compared to have a unified understanding of aptamer/AuNP systems.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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23
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Correction to: DNA Nanotechnology for Multimodal Synergistic Theranostics. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00190-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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24
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Xu X, Xiao L, Gu C, Shang J, Xiang Y. Wavelength-Selective Activation of Photocaged DNAzymes for Metal Ion Sensing in Live Cells. ACS OMEGA 2021; 6:13153-13160. [PMID: 34056465 PMCID: PMC8158819 DOI: 10.1021/acsomega.1c00976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 05/09/2023]
Abstract
RNA-cleaving DNAzymes are widely applied as sensors for detecting metal ions in environmental samples owing to their high sensitivity and selectivity, but their use for sensing biological metal ions in live cells is challenging because constitutive sensors fail to report the spatiotemporal heterogeneity of biological processes. Photocaged DNAzymes can be activated by light for sensing purposes that need spatial and temporal resolution. Studying complex biological processes requires logic photocontrol, but unfortunately all the literature-reported photocaged DNAzymes working in live cells cannot be selectively controlled by light irradiation at different wavelengths. In this work, we developed photocaged DNAzymes responsive to UV and visible light using a general synthetic method based on phosphorothioate chemistry. Taking the Zn2+-dependent DNAzyme sensor as a model, we achieved wavelength-selective activation of photocaged DNAzymes in live human cells by UV and visible light, laying the groundwork for the logic activation of DNAzyme-based sensors in biological systems.
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25
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Gu C, Xiao L, Shang J, Xu X, He L, Xiang Y. Chemical synthesis of stimuli-responsive guide RNA for conditional control of CRISPR-Cas9 gene editing. Chem Sci 2021; 12:9934-9945. [PMID: 34377390 PMCID: PMC8317661 DOI: 10.1039/d1sc01194d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas9 promotes changes in identity or abundance of nucleic acids in live cells and is a programmable modality of broad biotechnological and therapeutic interest. To reduce off-target effects, tools for conditional control of CRISPR-Cas9 functions are under active research, such as stimuli-responsive guide RNA (gRNA). However, the types of physiologically relevant stimuli that can trigger gRNA are largely limited due to the lack of a versatile synthetic approach in chemistry to introduce diverse labile modifications into gRNA. In this work, we developed such a general method to prepare stimuli-responsive gRNA based on site-specific derivatization of 2′-O-methylribonucleotide phosphorothioate (PS-2′-OMe). We demonstrated CRISPR-Cas9-mediated gene editing in human cells triggered by oxidative stress and visible light, respectively. Our study tackles the synthetic challenge and paves the way for chemically modified RNA to play more active roles in gene therapy. Conditional control of CRISPR-Cas9 activity by reactive oxygen species and visible light is achieved using stimuli-responsive guide RNA synthesized by a general method based on RNA 2′-O-methylribonucleotide phosphorothioate.![]()
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Affiliation(s)
- Chunmei Gu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Lu Xiao
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Xiao Xu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Luo He
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
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27
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Comparison of visual detection of melamine by AuNPs sol prepared in marine and terrestrial plant extracts. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Abstract
The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.
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Affiliation(s)
- Xingyi Ma
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
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29
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Xu W, He W, Du Z, Zhu L, Huang K, Lu Y, Luo Y. Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications. Angew Chem Int Ed Engl 2021; 60:6890-6918. [PMID: 31729826 PMCID: PMC9205421 DOI: 10.1002/anie.201909927] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/29/2019] [Indexed: 01/01/2023]
Abstract
Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.
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Affiliation(s)
- Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Wanchong He
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana, Illinois 61801 (USA)
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
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30
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Saran R, Huang Z, Liu J. Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Wu S, Lei L, Xia Y, Oliver S, Chen X, Boyer C, Nie Z, Shi S. PNIPAM-immobilized gold-nanoparticles with colorimetric temperature-sensing and reusable temperature-switchable catalysis properties. Polym Chem 2021. [DOI: 10.1039/d1py01180d] [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
The temperature-responsive core–shell hybrid nanoparticles PNIPAMs-AuNP have dual-functional applications as colorimetric temperature-sensors and reusable temperature-switchable catalysts.
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Affiliation(s)
- Si Wu
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lei Lei
- Centre for Advanced Macromolecular Design, School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yuzheng Xia
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Susan Oliver
- Centre for Advanced Macromolecular Design, School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Xiaonong Chen
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Cyrille Boyer
- Centre for Advanced Macromolecular Design, School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Zhiyong Nie
- Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, 100850, China
| | - Shuxian Shi
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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32
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Yang M, Chen X, Su Y, Liu H, Zhang H, Li X, Xu W. The Fluorescent Palette of DNA-Templated Silver Nanoclusters for Biological Applications. Front Chem 2020; 8:601621. [PMID: 33262973 PMCID: PMC7686567 DOI: 10.3389/fchem.2020.601621] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
Recently years have witnessed a surge in application of DNA-AgNCs in optics, catalysis, sensing, and biomedicine. DNA-templated silver nanoclusters (DNA-AgNCs), as emerging fluorophores, display superior optical performance since their size is close to the Fermi wavelength. DNA-AgNCs possess unique features, including high fluorescence quantum yields and stability, biocompatibility, facile synthesis, and low toxicity, which are requisite for fluorescent probes. The fluorescent emission of DNA-AgNCs can cover the violet to near-infrared (NIR) region by varying the DNA sequences, lengths, and structures or by modifying the environmental factors (such as buffer, pH, metal ions, macromolecular polymers, and small molecules). In view of the above excellent properties, we overview the DNA-AgNCs from the viewpoints of synthesis and fluorescence properties, and summarized its biological applications of fluorescence sensing and imaging.
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Affiliation(s)
- Min Yang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Xu Chen
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
| | - Yuan Su
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
| | - Haiyan Liu
- Faculty of Public Health, North China University of Technology, Tangshan, China
| | - Hongxing Zhang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Xiangyang Li
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Wentao Xu
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
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33
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Huang Z, Zhao Y, Liu B, Guan S, Liu J. Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13708-13715. [PMID: 33161721 DOI: 10.1021/acs.langmuir.0c02761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.
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Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yu Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Shaokang Guan
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Moon WJ, Yang Y, Liu J. Zn 2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications. Chembiochem 2020; 22:779-789. [PMID: 33007113 DOI: 10.1002/cbic.202000586] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/01/2020] [Indexed: 12/20/2022]
Abstract
Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn2+ is a very important one among them. Zn2+ has good biocompatibility and can be used for intracellular applications. Chemically, Zn2+ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn2+ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn2+ a unique cofactor for DNAzyme reactions. This review summarizes Zn2+ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn2+ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn2+ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn2+ , which can facilitate practical applications of Zn2+ -dependent DNAzymes.
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Affiliation(s)
- Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Yongjie Yang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.,Department of Food and Biological Science, College of Agricultural, Yanbian University, Yanbian Chaoxianzuzizhizhou, Yanji, 133002, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.,Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, China
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35
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Hu S, Huang PJJ, Wang J, Liu J. Dissecting the Effect of Salt for More Sensitive Label-Free Colorimetric Detection of DNA Using Gold Nanoparticles. Anal Chem 2020; 92:13354-13360. [PMID: 32856891 DOI: 10.1021/acs.analchem.0c02688] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Taking advantage of the protection effect of single-stranded DNA oligonucleotides, gold nanoparticles (AuNPs) remain dispersed and retain a red color with the addition of a low concentration of salt, while AuNPs would aggregate in the presence of double-stranded DNA. This difference has been used to design label-free colorimetric sensors for DNA detection. NaCl is the most commonly used salt to induce the aggregation of AuNPs. In this work, we aimed to test if other salts can provide even better sensor performance and to understand the effects of the cations and anions in salts. We first studied the effect of anions, including halides (NaF, NaCl, NaBr, and NaI), and other common salts (NaNO3, NaClO4, Na2SO4, Na2S2O3, sodium phosphate, and sodium citrate). Among them, weakly adsorbing ones such as F-, citrate, and phosphate appeared to yield better sensitivity than Cl-. Anions can directly adsorb on the AuNPs and affect DNA adsorption. We then tested cations, and only group 1A metals (LiCl, NaCl, KCl, RbCl, and CsCl) can signal DNA adsorption, while divalent metals (MgCl2, CaCl2, MnCl2, and NiCl2) barely showed the effect of DNA. CsCl only works for strongly adsorbing DNA, such as A15, but not weakly adsorbing T15. Overall, NaF is a better salt than NaCl by having a 2.3-fold higher sensitivity, which was confirmed in a DNA sensing assay. This work has identified a better salt yielding higher sensitivity, and sensing work relying on the change of the aggregation state of AuNPs can benefit from this study.
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Affiliation(s)
- Shengqiang Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jianxiu Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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36
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Guo X, Li F, Liu C, Zhu Y, Xiao N, Gu Z, Luo D, Jiang J, Yang D. Construction of Organelle‐Like Architecture by Dynamic DNA Assembly in Living Cells. Angew Chem Int Ed Engl 2020; 59:20651-20658. [DOI: 10.1002/anie.202009387] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaocui Guo
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Chunxia Liu
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Nannan Xiao
- State Key Laboratory of Medicinal Chemical Biology Nankai University Tianjin 300350 P. R. China
| | - Zi Gu
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Dan Luo
- Department of Biological &Environmental Engineering Cornell University Ithaca NY 14853 USA
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing & Chemometrics College of Chemistry & Chemical Engineering Hunan University Changsha 410082 P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
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37
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Guo X, Li F, Liu C, Zhu Y, Xiao N, Gu Z, Luo D, Jiang J, Yang D. Construction of Organelle‐Like Architecture by Dynamic DNA Assembly in Living Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Xiaocui Guo
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Chunxia Liu
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Nannan Xiao
- State Key Laboratory of Medicinal Chemical Biology Nankai University Tianjin 300350 P. R. China
| | - Zi Gu
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Dan Luo
- Department of Biological &Environmental Engineering Cornell University Ithaca NY 14853 USA
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing & Chemometrics College of Chemistry & Chemical Engineering Hunan University Changsha 410082 P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
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38
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Xu W, He W, Du Z, Zhu L, Huang K, Lu Y, Luo Y. Funktionelle Nukleinsäure‐Nanomaterialien: Entwicklung, Eigenschaften und Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Wanchong He
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Yi Lu
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
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39
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Zhao Y, Feng Y, Zhang Y, Xia P, Xiao Z, Wang Z, Yan H. Combining competitive sequestration with nonlinear hybridization chain reaction amplification: an ultra-specific and highly sensitive sensing strategy for single-nucleotide variants. Anal Chim Acta 2020; 1130:107-116. [PMID: 32892930 DOI: 10.1016/j.aca.2020.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Highly specific and sensitive detection of single-nucleotide variants (SNVs) is of central importance in disease diagnosis and pharmacogenomics. However, it remains a great challenge to successfully detect very low amounts of mutant SNV sequences in real samples in which a SNV sequence may be surrounded by high levels of closely related wild-type sequences. Herein, we propose an ultra-specific and highly sensitive SNV sensing strategy by combining the competitive sequestration with the nonlinear hybridization chain reaction (HCR) amplification. The rationally designed sequestration hairpin can effectively sequester the large amount of wild-type sequence and thus dramatically improve the hybridization specificity in recognizing SNVs. To improve the detection sensitivity, a new fluorescent signal probe is fabricated by intercalating SYBR Green I dye into the nonlinear HCR based DNA dendrimer to further bind with SNVs for signal amplification. The hyperbranched DNA dendrimer possesses large numbers of DNA duplexes for dye intercalation, thus the signal probe shows strong fluorescence intensity, leading to large fluorescence signal amplification. Taking advantage of the improved hybridization specificity of the competitive sequestration and the enhanced fluorescence response of the nonlinear HCR amplification, the developed sensing strategy enables ultra-specific and highly sensitive detection of SNVs. Taking human pancreatic cancers and colorectal carcinomas related KRAS gene mutations as models, the developed strategy shows remarkably high specificity against 17 SNVs (discrimination factors ranged from 126 to 1001 with a median of 310), and achieves high sensitivity for 6 KRAS mutations (the best resultant detection limit reached 15 pM for KRAS G13D (c.38G > A)). Notably, combined with PCR amplification, our SNV sensing strategy could detect KRAS G12D (c.35G > A) from extracted human genomic DNA samples at abundance as low as 0.05%. This work expands the rule set of designing specific and sensitive SNV sensing strategies and shows promising potential application in clinical diagnosis.
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Affiliation(s)
- Yan Zhao
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
| | - Yuanbo Feng
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yuanbo Zhang
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Pu Xia
- Key Laboratory of Spectral Imaging Technology, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Zihan Xiao
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Ziheng Wang
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Hongxia Yan
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
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40
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Metal organic framework coated MnO2 nanosheets delivering doxorubicin and self-activated DNAzyme for chemo-gene combinatorial treatment of cancer. Int J Pharm 2020; 585:119513. [DOI: 10.1016/j.ijpharm.2020.119513] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/22/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023]
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41
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Liu X, He F, Zhang F, Zhang Z, Huang Z, Liu J. Dopamine and Melamine Binding to Gold Nanoparticles Dominates Their Aptamer-Based Label-Free Colorimetric Sensing. Anal Chem 2020; 92:9370-9378. [PMID: 32515584 DOI: 10.1021/acs.analchem.0c01773] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Target-directed aptamer adsorption by gold nanoparticles (AuNPs) has been widely used to develop label-free colorimetric biosensors. However, the potential interactions between target molecules and AuNPs have not been considered, which may lead to misinterpretation of analytical results. In this work, the detection of dopamine, melamine, and K+ was studied as model systems to address this problem. First, dopamine and two control molecules all induced the aggregation of citrate-capped AuNPs with apparent Kd's of 5.8 μM dopamine, 51.6 μM norepinephrine, and 142 μM tyramine. Isothermal titration calorimetry measured the aptamer Kd to be 1.9 μM dopamine and 16.8 μM norepinephrine, whereas tyramine cannot bind. Surface enhanced Raman spectroscopy confirmed direct adsorption of dopamine, and the adsorbed dopamine inhibited the adsorption of DNA. Using a typical salt-induced colorimetric detection protocol, a similar color response was observed regardless of the sequence of DNA, indicating the observed color change reflected the adsorption of dopamine by the AuNPs instead of the binding of dopamine by the aptamer. For this label-free sensor to work, the interaction between the target molecule and AuNPs should be very weak, while dopamine represents an example of strong interactions. For the other two systems, the melamine detection did not reflect aptamer binding either but the K+ detection did, suggesting melamine also strongly interacted with AuNPs, whereas K+ had very weak interactions with AuNPs. Since each target molecule is different, such target/AuNP interactions need to be studied case-by-case to ensure the sensing mechanism.
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Affiliation(s)
- Xixia Liu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei 425002, China.,Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Fan He
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,College of Food Science, Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong P. R. China
| | - Fang Zhang
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Zijie Zhang
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Zhicheng Huang
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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42
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Chen X, He F, Fang W, Shen J, Liu X, Xue Y, Liu H, Li J, Wang L, Li Y, Fan C. DNA-Guided Room-Temperature Synthesis of Single-Crystalline Gold Nanostructures on Graphdiyne Substrates. ACS CENTRAL SCIENCE 2020; 6:779-786. [PMID: 32490194 PMCID: PMC7256954 DOI: 10.1021/acscentsci.0c00223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Indexed: 05/27/2023]
Abstract
Nobel metal nanoparticles with tunable morphologies are highly desirable due to their unique electronic, magnetic, optical, and/or catalytic features. Here we report the use of multilayered graphdyine (GD) as a substrate for the reductant-free, room-temperature synthesis of single-crystal Au nanostructures with tunable morphology. We find that the GD template rich in sp-carbon atoms possesses high affinity with Au atoms on the {111} facets, and that the intrinsic reductivity of GD facilitates the rapid growth of Au nanoplates. The introduction of single-stranded DNA strands further results in the synthesis of Au nanostructures with decreased anisotropy, i.e., polygons and flower-like nanoparticles. The DNA-guided tunable Au growth arises from the strong adsorption of DNA on the GD template that alters the uniformity of the interface, which provides a direct route to synthesize Au nanostructures with tailorable morphology and photonic properties.
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Affiliation(s)
- Xiaoliang Chen
- Division
of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial
Physics and Technology, Shanghai Institute of Applied Physics, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, Shanghai 201800, China
| | - Feng He
- Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Weina Fang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200024, China
| | - Jianlei Shen
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200024, China
| | - Xiaoguo Liu
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200024, China
| | - Yurui Xue
- Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Huibiao Liu
- Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiang Li
- Division
of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial
Physics and Technology, Shanghai Institute of Applied Physics, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, Shanghai 201800, China
- Shanghai
Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy
of Sciences, Shanghai 201204, China
| | - Lihua Wang
- Division
of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial
Physics and Technology, Shanghai Institute of Applied Physics, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, Shanghai 201800, China
- Shanghai
Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy
of Sciences, Shanghai 201204, China
| | - Yuliang Li
- Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunhai Fan
- Division
of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial
Physics and Technology, Shanghai Institute of Applied Physics, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, Shanghai 201800, China
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200024, China
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43
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He MQ, Chen S, Meng J, Shi W, Wang K, Yu YL, Wang JH. Capping Ligand Size-Dependent LSPR Property Based on DNA Nanostructure-Mediated Morphological Evolution of Gold Nanorods for Ultrasensitive Visualization of Target DNA. Anal Chem 2020; 92:7054-7061. [PMID: 32337976 DOI: 10.1021/acs.analchem.0c00321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Systematically tuning the structures and properties of noble-metal nanoparticles through biomolecule-mediated overgrowth is of significant importance for their applications in biosensing and imaging. Herein thiolated biomolecules with different concentrations and sizes (molecular weight and spatial structure) were used as a class of capping ligands to control the longitudinal surface plasmon resonance (LSPR) property of gold nanorods (GNRs). The LSPR peaks were red-shifted by increasing the capping agent concentration. The size effect could be divided to two aspects: (1) When the ligands are small molecules, the LSPR peak is blue-shifted as the size of the capping ligand increases. (2) When the ligands are macromolecular proteins, the LSPR property is similar to that of the overgrown nanoparticle (Au@gap@GNR) without thiolated biomolecules as capping agents. Interestingly, thiol-free and nonhomooligomeric DNA strands as capping agents present a similar influence in shaping the overgrowth of GNRs by varying their concentrations and sizes. In addition, the size effect of a DNA nanostructure was used to construct a ΔλLSPR-based catalytic nucleic acid biosensor using a DNA dendritic nanostructure as a capping agent combined with LSPR signals generated from the Au@gap@GNRs with morphological evolution. More importantly, the ΔλLSPR-based biosensor possesses three advantages in nucleic acid biosensing: (1) It is completely label- and wash-free, (2) it has an ultrahigh sensitivity and signal-to-noise ratio, and (3) it can be visualized without any instrumental aid, indicating a significant potential for ultrasensitive biosensing.
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Affiliation(s)
- Meng-Qi He
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Shuai Chen
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China
| | - Jie Meng
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Wei Shi
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Kun Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
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44
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Yang H, Peng D, Zhou Y, Liu J. Pb 2+ as a Substrate and a Cofactor of a Porphyrin Metalation DNAzyme. Chembiochem 2020; 21:2259-2263. [PMID: 32202058 DOI: 10.1002/cbic.202000073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/21/2020] [Indexed: 11/11/2022]
Abstract
We herein report a DNAzyme named T30695 (sequence: (G3 T)4 ) that can catalyze Zn2+ insertion into three different porphyrins in the presence of Pb2+ as a cofactor. Meanwhile, T30695 with Pb2+ alone was found to cause a shift in both the fluorescence and UV-vis spectra of protoporphyrin IX (PPIX), thus suggesting that metalation of Pb2+ was also achieved at room temperature. From kinetic measurements, the reaction required two Pb2+ ions; this is consistent with one being a cofactor and the other being a substrate. No previous reports inserted Pb2+ into porphyrins by using DNAzymes or protein-based enzymes. This reaction was most significantly inhibited in the presence of K+ followed by Na+ and Li+ , suggesting the importance of the Pb2+ -stabilized G-quadruplex. When Pb2+ is inserted into PPIX, its emission blue shifts from 635 to 590 nm, thus allowing simple ratiometric fluorescent sensing with a detection limit of 1.2 nM Pb2+ .
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei, 434025, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Dong Peng
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada.,College of Chemistry20, Nanchang University, 999 Xuefu Avenue, Nanchang, 330031, Jiangxi, China
| | - Yu Zhou
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei, 434025, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
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45
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Encoding quantized fluorescence states with fractal DNA frameworks. Nat Commun 2020; 11:2185. [PMID: 32366822 PMCID: PMC7198603 DOI: 10.1038/s41467-020-16112-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/14/2020] [Indexed: 02/02/2023] Open
Abstract
Signal amplification in biological systems is achieved by cooperatively recruiting multiple copies of regulatory biomolecules. Nevertheless, the multiplexing capability of artificial fluorescent amplifiers is limited due to the size limit and lack of modularity. Here, we develop Cayley tree-like fractal DNA frameworks to topologically encode the fluorescence states for multiplexed detection of low-abundance targets. Taking advantage of the self-similar topology of Cayley tree, we use only 16 DNA strands to construct n-node (n = 53) structures of up to 5 megadalton. The high level of degeneracy allows encoding 36 colours with 7 nodes by site-specifically anchoring of distinct fluorophores onto a structure. The fractal topology minimises fluorescence crosstalk and allows quantitative decoding of quantized fluorescence states. We demonstrate a spectrum of rigid-yet-flexible super-multiplex structures for encoded fluorescence detection of single-molecule recognition events and multiplexed discrimination of living cells. Thus, the topological engineering approach enriches the toolbox for high-throughput cell imaging. Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.
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46
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Huang C, Chen X, Xue Z, Wang T. Effect of structure: A new insight into nanoparticle assemblies from inanimate to animate. SCIENCE ADVANCES 2020; 6:eaba1321. [PMID: 32426506 PMCID: PMC7220353 DOI: 10.1126/sciadv.aba1321] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/27/2020] [Indexed: 05/03/2023]
Abstract
Nanoparticle (NP) assemblies are among the foremost achievements of nanoscience and nanotechnology because their interparticle interactions overcome the weaknesses displayed by individual NPs. However, previous studies have considered NP assemblies as inanimate, which had led to their dynamic properties being overlooked. Animate properties, i.e., those mimicking biological properties, endow NP ensembles with unique and unexpected functionalities for practical applications. In this critical review, we highlight recent advances in our understanding of the properties of NP assemblies, particularly their animate properties. Key examples are used to illustrate critical concepts, and special emphasis is placed on animate property-dependent applications. Last, we discuss the barriers to further advances in this field.
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Affiliation(s)
- Chuanhui Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry, Chinese Academy of Sciences, #2 Zhongguancun, North First Street, Beijing 100190, China
| | - Xiangyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry, Chinese Academy of Sciences, #2 Zhongguancun, North First Street, Beijing 100190, China
| | - Zhenjie Xue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry, Chinese Academy of Sciences, #2 Zhongguancun, North First Street, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry, Chinese Academy of Sciences, #2 Zhongguancun, North First Street, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author.
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47
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Huang Z, Liu B, Liu J. A high local DNA concentration for nucleating a DNA/Fe coordination shell on gold nanoparticles. Chem Commun (Camb) 2020; 56:4208-4211. [PMID: 32168370 DOI: 10.1039/d0cc01418d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Preparing DNA/Fe coordination nanoparticles in solution requires a high concentration of DNA. Herein we grew a DNA/Fe shell on DNA-functionalized gold nanoparticles. Taking advantage of the high local DNA density, the required DNA concentration decreased 60-fold, and the size can be controlled. This hybrid material allowed drug loading and colorimetric sensing.
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Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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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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49
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Wu R, Peng H, Zhu JJ, Jiang LP, Liu J. Attaching DNA to Gold Nanoparticles With a Protein Corona. Front Chem 2020; 8:121. [PMID: 32161750 PMCID: PMC7052371 DOI: 10.3389/fchem.2020.00121] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/10/2020] [Indexed: 12/24/2022] Open
Abstract
DNA-functionalized gold nanoparticles (AuNPs) have been widely used in directed assembly of materials, biosensors, and drug delivery. This conjugate may encounter proteins in these applications and proteins may affect not only DNA adsorption but also the function of the attached DNA. Bovine serum albumin (BSA) with many cysteine residues can strongly adsorb on AuNPs and this conjugate showed high colloidal stability against salt, acid and base. Similar protection effects were also observed with a few other common proteins including catalase, hemoglobin, glucose oxidase, and horseradish peroxidase. DNA oligonucleotides without a thiol label can hardly displace adsorbed BSA, and BSA cannot displace pre-adsorbed DNA either, indicating a strongly kinetically controlled system. Thiolated DNA can be attached at a low density on the AuNPs with a BSA corona. The BSA corona did not facilitate the hybridization of the conjugated DNA, while a smaller peptide, glutathione allowed faster hybridization. Overall, proteins increase the colloidal stability of AuNPs, and they do not perturb the gold-thiol bond in the DNA conjugate, although a large protein corona may inhibit the hybridization function of DNA.
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Affiliation(s)
- Rong Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Huaping Peng
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.,Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
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Chang Y, Liu B, Huang Z, Liu Y, Liu M, Liu J. Yttrium Oxide as a Strongly Adsorbing but Nonquenching Surface for DNA Oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1034-1042. [PMID: 31935105 DOI: 10.1021/acs.langmuir.9b02743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A large number of nanomaterials can strongly adsorb DNA and quench fluorescence, such as graphene oxide, gold nanoparticles, and most metal oxides. On the other hand, noncationic nanomaterials that adsorb DNA but cannot quench fluorescence are less known. These materials are attractive for studying the mechanism of DNA-based surface reactions. Y2O3 was found to have this property. Herein, we used fluorescently labeled oligonucleotides as probes to study the mechanism of DNA adsorption. The fluorescence was quenched at low concentrations of Y2O3 and then recovered and even enhanced with higher Y2O3 concentrations. The reason was attributed to the intermolecular quenching by the DNA bases of the neighboring strands. The fluorescence enhancement was due to breaking of the intramolecular fluorophore/DNA interactions, and the most enhancement was observed with a Cy3-labeled DNA. DNA adsorption followed the Langmuir isotherm on Y2O3. Desorption experiments suggested that DNA was adsorbed through the phosphate backbone, with FAM-G15 and FAM-C15 adsorbed more strongly than the other two DNA homopolymers. With a high salt concentration, no fluorescence change was observed, suggesting that the DNA adsorbed in a folded state reducing intermolecular quenching. Overall, Y2O3 might be useful as a model surface for investigating DNA hybridization on a surface.
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Affiliation(s)
- Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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