1
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Song T, Cooper L, Galván Achi J, Wang X, Dwivedy A, Rong L, Wang X. Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition. J Am Chem Soc 2024; 146:5894-5900. [PMID: 38408177 PMCID: PMC10965196 DOI: 10.1021/jacs.3c11760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Coronavirus transmission and mutations have brought intensive challenges on pandemic control and disease treatment. Developing robust and versatile antiviral drugs for viral neutralization is highly desired. Here, we created a new polyvalent nanobody (Nb) structure that shows the effective inhibition of SARS-CoV-2 infections. Our polyvalent Nb structure, called "PNS", is achieved by first conjugating single-stranded DNA (ssDNA) and the receptor-binding domain (RBD)-targeting Nb with retained binding ability to SARS-CoV-2 spike protein and then coalescing the ssDNA-Nb conjugates around a gold nanoparticle (AuNP) via DNA hybridization with a desired Nb density that offers spatial pattern-matching with that of the Nb binding sites on the trimeric spike. The surface plasmon resonance (SPR) assays show that the PNS binds the SARS-CoV-2 trimeric spike proteins with a ∼1000-fold improvement in affinity than that of monomeric Nbs. Furthermore, our viral entry inhibition assays using the PNS against SARS-CoV-2 WA/2020 and two recent variants of interest (BQ1.1 and XBB) show an over 400-fold enhancement in viral inhibition compared to free Nbs. Our PNS strategy built on a new DNA-protein conjugation chemistry provides a facile approach to developing robust virus inhibitors by using a corresponding virus-targeting Nb with a desired Nb density.
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Affiliation(s)
- Tingjie Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jazmin Galván Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xiaojing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhisek Dwivedy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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2
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Sun X, Yao D, Liang H. pH-Controlled Resettable Modular DNA Strand-Displacement Circuits. NANO LETTERS 2023; 23:11540-11547. [PMID: 38085915 DOI: 10.1021/acs.nanolett.3c03265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Sophisticated dynamic molecular systems with diverse functions have been fabricated by using the fundamental tool of toehold-mediated strand displacement (TMSD) in the field of dynamic DNA nanotechnology. However, simple approaches to reset these TMSD-based dynamic systems are lacking due to the difficulty in creating kinetically favored pathways to implement the backward resetting reactions. Here, we develop a facile proton-driven strategy to achieve complete resetting of a modular DNA circuit by integrating a pH-responsive intermolecular CG-C+ triplex DNA and an i-motif DNA into the conventional DNA substrate. The pH-programmed strategy allows modular DNA components to specifically associate/dissociate to promote the forward/backward TMSD reactions, thereby enabling the modular DNA circuit to be repeatedly operated at a constant temperature without generating any DNA waste products. Leveraging this tractable approach, we further constructed two resettable DNA logic gates used for logical computation and two resettable catalytic DNA systems with good performance in signal transduction and amplification.
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Affiliation(s)
- Xiaoyun Sun
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dongbao Yao
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
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3
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Wang X, Shepherd S, Li N, Che C, Song T, Xiong Y, Palm IR, Zhao B, Kohli M, Demirci U, Lu Y, Cunningham BT. A Target Recycling Amplification Process for the Digital Detection of Exosomal MicroRNAs through Photonic Resonator Absorption Microscopy. Angew Chem Int Ed Engl 2023; 62:e202217932. [PMID: 36622783 PMCID: PMC10073263 DOI: 10.1002/anie.202217932] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/10/2023]
Abstract
Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of miRNAs using photonic resonator absorption microscopy. We achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. Compared with traditional qRT-PCR, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulating miRNA biomarker quantification, where the miRNAs are present in low concentrations or sample volume, with potentials for frequent, low-cost, and minimally invasive point-of-care testing.
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Affiliation(s)
- Xiaojing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nantao Li
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Congnyu Che
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Tingjie Song
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yanyu Xiong
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Isabella Rose Palm
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Bin Zhao
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Manish Kohli
- Department of Oncology, Mayo Clinic Rochester, MN 55905, USA; Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 12902, USA
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Yi Lu
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Brian T. Cunningham
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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4
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Toehold-mediated biosensors: Types, mechanisms and biosensing strategies. Biosens Bioelectron 2022; 220:114922. [DOI: 10.1016/j.bios.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
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5
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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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6
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Yu S, Shang J, He S, Wang Q, Li R, Chen Y, Liu X, Wang F. Multiply Guaranteed and Successively Amplified Activation of a Catalytic DNA Machine for Highly Efficient Intracellular Imaging of MicroRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203341. [PMID: 35843889 DOI: 10.1002/smll.202203341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/24/2022] [Indexed: 06/15/2023]
Abstract
DNA amplification machines show great promise for intracellular imaging, yet are always constrained by off-site machinery activation or signal leakage, originating from the inherent thermodynamically driven hybridization between machinery substrates. Herein, an entropy-driven catalytic DNA amplification machine is integrated with the on-site amplified substrate exposure procedure to realize the high-contrast in vivo imaging of microRNA (miRNA). The key machinery substrate (fuel strands) is initially split into substrate subunits that are respectively grafted into an auxiliary DNA polymerization amplification accessory for eliminating the undesired signal leakage. Meanwhile, in target cells, the auxiliary polymerization accessory can be motivated by cell-specific mRNA for successively restoring their intact machine-propelling functions for guaranteeing the on-site amplified imaging of miRNA with high specificity. This intelligent on-site multiply guaranteed machinery can improve the specificity of catalytic DNA machines for discriminating different cell types and, thus, can provide a remarkable prospect in biomedical diagnosis.
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Affiliation(s)
- Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430072, China
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7
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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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8
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Zheng B, Dong H, Zhu J, Zhang Q, Yang S, Yao D. A rational design of a cascaded DNA circuit for nanoparticle assembly and its application in the discrimination of single-base changes. J Mater Chem B 2022; 10:4561-4567. [PMID: 35621087 DOI: 10.1039/d2tb00155a] [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
In the field of dynamic DNA nanotechnology, a designable DNA assembly circuit based on the toehold-mediated strand displacement reaction has demonstrated its ability to program the self-assembly of nanoparticles. However, the laborious work for the modification of nanoparticles with oligonucleotides, the long assembly time, and the circuit leakage prevent its further and scalable applications. To this end, cascaded circuits composed of two recycling circles are rationally designed in this study. Through the pre-initiation of the autonomous reaction, nanoparticles as sensing elements and no additionally exposed bases on the substrate hybridized with fuel strand, the real assembly time and signal leakage for diagnostic application can be effectively reduced and eliminated, thus offering a promising methodology for future point-of-care testing.
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Affiliation(s)
- Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Huaze Dong
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Jinmiao Zhu
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Qi Zhang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Shiwei Yang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Dongbao Yao
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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9
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Zheng J, Cheng X, Zhang H, Bai X, Ai R, Shao L, Wang J. Gold Nanorods: The Most Versatile Plasmonic Nanoparticles. Chem Rev 2021; 121:13342-13453. [PMID: 34569789 DOI: 10.1021/acs.chemrev.1c00422] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gold nanorods (NRs), pseudo-one-dimensional rod-shaped nanoparticles (NPs), have become one of the burgeoning materials in the recent years due to their anisotropic shape and adjustable plasmonic properties. With the continuous improvement in synthetic methods, a variety of materials have been attached around Au NRs to achieve unexpected or improved plasmonic properties and explore state-of-the-art technologies. In this review, we comprehensively summarize the latest progress on Au NRs, the most versatile anisotropic plasmonic NPs. We present a representative overview of the advances in the synthetic strategies and outline an extensive catalogue of Au-NR-based heterostructures with tailored architectures and special functionalities. The bottom-up assembly of Au NRs into preprogrammed metastructures is then discussed, as well as the design principles. We also provide a systematic elucidation of the different plasmonic properties associated with the Au-NR-based structures, followed by a discussion of the promising applications of Au NRs in various fields. We finally discuss the future research directions and challenges of Au NRs.
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Affiliation(s)
- Jiapeng Zheng
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Xizhe Cheng
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Han Zhang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Xiaopeng Bai
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Ruoqi Ai
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Lei Shao
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Jianfang Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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10
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Zhang XL, Yin Y, Du SM, Kong LQ, Chai YQ, Li ZH, Yuan R. Dual 3D DNA Nanomachine-Mediated Catalytic Hairpin Assembly for Ultrasensitive Detection of MicroRNA. Anal Chem 2021; 93:13952-13959. [PMID: 34613709 DOI: 10.1021/acs.analchem.1c03215] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Herein, we designed a dual 3D DNA nanomachine (DDNM)-mediated catalytic hairpin assembly (DDNM-CHA) to construct an electrochemical biosensor for ultrasensitive detection of miRNA, which possesses quite a faster reaction rate and much higher amplification efficiency than those of traditional catalytic hairpin assembly (CHA). Impressively, since the DDNM skillfully increases the local concentration of reactants and decreases the steric hindrance of substrates simultaneously, the DDNM-CHA could be endowed with higher collision efficiency and more effective reaction compared with traditional CHA, resulting in a hyper conversion efficiency up to 2.78 × 107 only in 25 min. This way, the developed DDNM-CHA could easily conquer the main predicaments: long reaction time and low efficiency. As a proof of the concept, we adopt the gold nanoparticles (AuNPs) and the magnetic nanoparticle (Fe3O4) as the kernel of DNM-A and DNM-B, respectively, and harness the magnetic electrode to directly adsorb the products H1-H2/Fe3O4 for constructing an immobilization-free biosensor for high-speed and ultrasensitive detection of miRNA with a detection limit of 0.14 fM. As a result, the DDNM-CHA we developed carves out a new insight to design a functional DNA nanomachine and evolve the analysis method for practical amplification in the sensing area and promotes the deeper exploration of the nucleic acid signal amplification strategy and DNA nanobiotechnology.
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Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yang Yin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Shu-Min Du
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Zhao-Hui Li
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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11
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Wang Z, Hu Y, Pan L. Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhiyu Wang
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology 1037 Luoyu Road Wuhan 430074 China
| | - Yingxin Hu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology 1037 Luoyu Road Wuhan 430074 China
- College of Information Science and Technology Shijiazhuang Tiedao University Shijiazhuang 050043 China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology 1037 Luoyu Road Wuhan 430074 China
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12
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Wang Z, Hu Y, Pan L. Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design. Angew Chem Int Ed Engl 2020; 59:14979-14985. [PMID: 32396703 DOI: 10.1002/anie.202005193] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/10/2020] [Indexed: 12/22/2022]
Abstract
Toehold-mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold-mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold-mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one-to-many and many-to-one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold-mediated DNA strand displacement.
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Affiliation(s)
- Zhiyu Wang
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, China
| | - Yingxin Hu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, China.,College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, 050043, China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, China
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13
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Guo Y, Yao D, Zheng B, Sun X, Zhou X, Wei B, Xiao S, He M, Li C, Liang H. pH-Controlled Detachable DNA Circuitry and Its Application in Resettable Self-Assembly of Spherical Nucleic Acids. ACS NANO 2020; 14:8317-8327. [PMID: 32579339 DOI: 10.1021/acsnano.0c02329] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Toehold-mediated strand displacement reaction, the fundamental basis in dynamic DNA nanotechnology, has proven its extraordinary power in programming dynamic molecular systems. Programmed activation of the toehold in a DNA substrate is crucial for building sophisticated DNA devices with digital and dynamic behaviors. Here we developed a detachable DNA circuit by embedding a pH-controlled intermolecular triplex between the toehold and branch migration domain of the traditional "linear substrate". The reaction rate and the "on/off" state of the detachable circuit can be regulated by varying the pHs. Similarly, a two-input circuit composed of three pH-responsive DNA modules was then constructed. Most importantly, a resettable self-assembly system of spherical nucleic acids was built by utilizing the high detachability of the intermolecular triplex structure-based DNA circuit. This work demonstrated a dynamic DNA device that can be repeatedly operated at constant temperature without generating additional waste DNA products. Moreover, this strategy showed an example of recycling waste spherical nucleic acids from a self-assembly system of spherical nucleic acids. Our strategy will provide a facile approach for dynamic regulation of complex molecular systems and reprogrammable nanoparticle assembly structures.
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Affiliation(s)
- Yijun Guo
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, People's Republic of China
| | - Xianbao Sun
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Bing Wei
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Miao He
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Chengxu Li
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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14
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Liang X, Li L, Tang J, Komiyama M, Ariga K. Dynamism of Supramolecular DNA/RNA Nanoarchitectonics: From Interlocked Structures to Molecular Machines. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200012] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Jiaxuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Katsuhiko Ariga
- WPI-MANA, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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15
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16
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Iglesias MS, Grzelczak M. Using gold nanoparticles to detect single-nucleotide polymorphisms: toward liquid biopsy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:263-284. [PMID: 32082965 PMCID: PMC7006498 DOI: 10.3762/bjnano.11.20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/21/2020] [Indexed: 05/02/2023]
Abstract
The possibility of detecting genetic mutations rapidly in physiological media through liquid biopsy has attracted the attention within the materials science community. The physical properties of nanoparticles combined with robust transduction methods ensure an improved sensitivity and specificity of a given assay and its implementation into point-of-care devices for common use. Covering the last twenty years, this review gives an overview of the state-of-the-art of the research on the use of gold nanoparticles in the development of colorimetric biosensors for the detection of single-nucleotide polymorphism as cancer biomarker. We discuss the main mechanisms of the assays that either are assisted by DNA-based molecular machines or by enzymatic reactions, summarize their performance and provide an outlook towards future developments.
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Affiliation(s)
- María Sanromán Iglesias
- Centro de Física de Materiales CSIC-UPV/EHU and Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 5, 20018 Donostia-Sebastián, Spain
| | - Marek Grzelczak
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
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17
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18
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Cascaded DNA circuits-programmed self-assembly of spherical nucleic acids for high signal amplification. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9603-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Li Y, Mansour H, Wang T, Poojari S, Li F. Naked-Eye Detection of Grapevine Red-Blotch Viral Infection Using a Plasmonic CRISPR Cas12a Assay. Anal Chem 2019; 91:11510-11513. [PMID: 31478642 DOI: 10.1021/acs.analchem.9b03545] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Herein, we described a novel plasmonic CRISPR Cas12a assay for the visual, colorimetric detection of grapevine viral infections. Our assay generates rapid and specific colorimetric signals for nucleic acid amplicons by combining the unique target-induced incriminate single-stranded DNase activity of Cas12a with plasmon coupling of DNA functionalized gold nanoparticles. The practical applicability of our plasmonic assay was successfully demonstrated through the detection of emerging red-blotch viral infections in grapevine samples collected from commercial vineyards.
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Affiliation(s)
- Yongya Li
- College of Chemistry , Sichuan University , Chengdu , Sichuan 610064 , P.R. China.,Department of Chemistry, Centre for Biotechnology , Brock University , St. Catharines , Ontario L2S 3A1 , Canada
| | - Hayam Mansour
- Department of Chemistry, Centre for Biotechnology , Brock University , St. Catharines , Ontario L2S 3A1 , Canada.,Department of Cell Biology , National Research Centre , Cairo 12622 , Egypt
| | - Tony Wang
- Cool Climate Oenology and Viticulture Institute , Brock University , St. Catharines , Ontario L2S 3A1 , Canada
| | - Sudarsana Poojari
- Cool Climate Oenology and Viticulture Institute , Brock University , St. Catharines , Ontario L2S 3A1 , Canada
| | - Feng Li
- College of Chemistry , Sichuan University , Chengdu , Sichuan 610064 , P.R. China.,Department of Chemistry, Centre for Biotechnology , Brock University , St. Catharines , Ontario L2S 3A1 , Canada
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20
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Wei B, Yao D, Zheng B, Zhou X, Guo Y, Li X, Li C, Xiao S, Liang H. Facile Strategy for Visible Disassembly of Spherical Nucleic Acids Programmed by Catalytic DNA Circuits. ACS APPLIED MATERIALS & INTERFACES 2019; 11:19724-19733. [PMID: 31083902 DOI: 10.1021/acsami.9b02107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The programmable toehold-mediated DNA-strand-displacement reaction has demonstrated its extraordinary capability in driving the spherical nucleic acid assembly. Here, a facile strategy of integrating a DNA-strand-displacement-based DNA circuit with a universal spherical nucleic acid aggregate system was developed for the visible disassembly of spherical nucleic acids. This integrated system exhibited rapid colorimetric response and good sensitivity in the disassembly reaction and demonstrated its capability in the application of single nucleotide polymorphism discrimination. Moreover, an OR logic gate used for multiplex detection was constructed through combining the fixed spherical nucleic acid disassembly system with two DNA circuits. This strategy will have great potential in the fabrication of a portable low-cost DNA diagnostic kit, and it is also a very promising method to be used in other applications, such as complex DNA networks and programmable phase transformation of nanoparticle superlattices.
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Affiliation(s)
- Bing Wei
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Dongbao Yao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering , Hefei Normal University , Hefei , Anhui 230061 , P. R. China
| | - Xiang Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Yijun Guo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Xiang Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Chengxu Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Shiyan Xiao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Haojun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
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21
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Wang G, Akiyama Y, Kanayama N, Takarada T, Maeda M. Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles for Gene Diagnosis and Directed Assembly. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1309.ch006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Guoqing Wang
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yoshitsugu Akiyama
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Faculty of Industrial Science and Technology, Tokyo University of Science, 102-1 Tomino, Oshamambe-cho, Yamakoshi-gun, Hokkaido 049-3514, Japan
| | - Naoki Kanayama
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Medicine, Science and Technology, Shinshu University, 4-7-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
| | - Tohru Takarada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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22
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Li MX, Xu CH, Zhang N, Qian GS, Zhao W, Xu JJ, Chen HY. Exploration of the Kinetics of Toehold-Mediated Strand Displacement via Plasmon Rulers. ACS NANO 2018; 12:3341-3350. [PMID: 29578338 DOI: 10.1021/acsnano.7b08673] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA/RNA strand displacement is one of the most fundamental reactions in DNA and RNA circuits and nanomachines. In this work, we reported an exploration of the dynamic process of the toehold-mediated strand displacement via core-satellite plasmon rulers at the single-molecule level. Applying plasmon rulers with unlimited lifetime, single-strand displacement triggered by the invader that resulted in stepwise leaving of satellite from the core was continuously monitored by changes of scattering signal for hours. The kinetics of strand displacement in vitro with three different toehold lengths have been investigated. Also, the study revealed the difference in the kinetics of strand displacement between DNA/RNA and DNA/DNA duplexes. For the kinetics study in vivo, influence from the surrounding medium has been evaluated using both phosphate buffer and cell lysate. Applying core-satellite plasmon rulers with high signal/noise ratio, kinetics study in living cells proceeded for the first time, which was not possible by conventional methods with a fluorescent reporter. The plasmon rulers, which are flexible, easily constructed, and robust, have proven to be effective tools in exploring the dynamical behaviors of biochemical reactions in vivo.
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Affiliation(s)
- Mei-Xing Li
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Cong-Hui Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Nan Zhang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Guang-Sheng Qian
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
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23
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Zhang Y, Cheng M, Wang Y, Shi F. Constructing a Multiplexed DNA Pattern by Combining Precise Magnetic Manipulation and DNA-Driven Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1100-1108. [PMID: 28903006 DOI: 10.1021/acs.langmuir.7b02608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There is an urgent demand to construct multiplexed biomolecular patterns to obtain more biological information from a single experiment. However, with only limited reports focusing on defective top-down approaches, challenges remain to develop a bottom-up strategy for multiplexed patterning. To this end, a novel strategy has been proposed to fabricate multiplexed DNA patterns via macroscopic assembly through combined precise magnetic manipulation and DNA hybridization-driven self-assembly. Therefore, a multiplexed DNA pattern composed of glass fibers loaded with multiple specific strands of DNA was constructed, and its potential application in simultaneous detection of multiplex target DNA was demonstrated. Moreover, the fabricated multiplexed DNA pattern shows an erasable behavior because the hybridized DNA can be disassembled by strand displacement.
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Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
| | - Mengjiao Cheng
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
| | - Yue Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
| | - Feng Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing, 100029, China
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24
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Chen W, Fang X, Ye X, Li H, Cao H, Kong J. DNA nanomachine-assisted magnetic bead based target recycling and isothermal amplification for sensitive fluorescence determination of interferon-γ. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2511-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Dong J, Wu T, Xiao Y, Chen L, Xu L, Li M, Zhao M. Target-triggered transcription machinery for ultra-selective and sensitive fluorescence detection of nucleoside triphosphates in one minute. Biosens Bioelectron 2017; 100:333-340. [PMID: 28942346 DOI: 10.1016/j.bios.2017.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/06/2017] [Accepted: 09/17/2017] [Indexed: 01/02/2023]
Abstract
Nucleoside triphosphates (NTPs) play important roles in living organisms. However, no fluorescent assays are currently available to simply and rapidly detect multiple NTPs with satisfactory selectivity, sensitivity and low cost. Here we demonstrate for the first time a target-triggered in-vitro transcription machinery for ultra-selective, sensitive and instant fluorescence detection of multiple NTPs. The machinery assembles RNA polymerase, DNA template and non-target NTPs to convert the target NTP into equivalent RNA signal sequences which are monitored by the fluorescence enhancement of molecular beacon. The machinery offers excellent selectivity for the target NTP against NDP, NMP and dNTP. Notably, to accelerate the kinetics of the machinery while maintain its high specificity, we investigated the sequence of DNA templates systematically and established a set of guidelines for the design of the optimum DNA templates, which allowed for instant detection of the target NTP at fmol level in less than 1min. Furthermore, the machinery could be transformed into logic gates to study the coeffects of two NTPs in biosynthesis and real-time monitoring systems to reflect the distribution of NTP in nucleotide pools. These results provide very useful and low-cost tools for both biochemical tests and point-of-care analysis.
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Affiliation(s)
- Jiantong Dong
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Xiao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lu Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lei Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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26
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Huang X, Liu Y, Yung B, Xiong Y, Chen X. Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer. ACS NANO 2017; 11:5238-5292. [PMID: 28590117 DOI: 10.1021/acsnano.7b02618] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.
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Affiliation(s)
- Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yijing Liu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Bryant Yung
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
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27
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Wang X, Yan N, Song T, Wang B, Wei B, Lin L, Chen X, Tian H, Liang H. Robust Fuel Catalyzed DNA Molecular Machine for in Vivo MicroRNA Detection. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaojing Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Nan Yan
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Lin Lin
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Huayu Tian
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
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28
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Wang S, Yang F, Jin D, Dai Q, Tu J, Liu Y, Ning Y, Zhang GJ. Toehold Mediated One-Step Conformation-Switchable “Signal-On” Electrochemical DNA Sensing Enhanced with Homogeneous Enzymatic Amplification. Anal Chem 2017; 89:5349-5356. [PMID: 28452219 DOI: 10.1021/acs.analchem.6b05171] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Siqi Wang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Fan Yang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Dan Jin
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Qi Dai
- Huangjia
Lake Hospital, Hubei University of Chinese Medicine, 1 Huangjia
Lake West Road, Wuhan, Hubei 430065, China
| | - Jiyuan Tu
- School
of Pharmacy, Hubei University of Chinese Medicine, 1 Huangjia
Lake West Road, Wuhan, Hubei 430065, China
| | - Yanju Liu
- School
of Pharmacy, Hubei University of Chinese Medicine, 1 Huangjia
Lake West Road, Wuhan, Hubei 430065, China
| | - Yong Ning
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Guo-Jun Zhang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
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29
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Yang J, Dou B, Yuan R, Xiang Y. Aptamer/Protein Proximity Binding-Triggered Molecular Machine for Amplified Electrochemical Sensing of Thrombin. Anal Chem 2017; 89:5138-5143. [PMID: 28393515 DOI: 10.1021/acs.analchem.7b00827] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The development of convenient and sensitive methods without involving any enzymes or complex nanomaterials for the monitoring of proteins is of great significance in disease diagnostics. In this work, we describe the validation of a new aptamer/protein proximity binding-triggered molecular machinery amplification strategy for sensitive electrochemical assay of thrombin in complex serum samples. The sensing interface is prepared by self-assembly of three-stranded DNA complexes on the gold electrode. The association of two distinct functional aptamers with different sites of thrombin triggers proximity binding-induced displacement of one of the short single-stranded DNAs (ssDNAs) from the surface-immobilized three-stranded DNA complexes, exposing a prelocked toehold domain to hybridize with a methylene blue (MB)-tagged fuel ssDNA strand (MB-DNA). Subsequent toehold-mediated strand displacement by the MB-DNA leads to the release and recycling of the aptamer/protein complexes and the function of the molecular machine. Eventually, a large number of MB-DNA strands are captured by the sensor surface, generating drastically amplified electrochemical responses from the MB tags for sensitive detection of thrombin. Our signal amplified sensor is completely enzyme-free and shows a dynamic range from 5 pM to 1 nM with a detection limit of 1.7 pM. Such sensor also has a high specificity for thrombin assay in serum samples. By changing the affinity probe pairs, the developed sensor can be readily expanded as a more general platform for sensitive detection of different types of proteins.
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Affiliation(s)
- Jianmei Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Baoting Dou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
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30
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Guo Y, Wei B, Xiao S, Yao D, Li H, Xu H, Song T, Li X, Liang H. Recent advances in molecular machines based on toehold-mediated strand displacement reaction. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Rapisarda A, Giamblanco N, Marletta G. Kinetic discrimination of DNA single-base mutations by localized surface plasmon resonance. J Colloid Interface Sci 2017; 487:141-148. [DOI: 10.1016/j.jcis.2016.10.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 10/20/2022]
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32
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Yao D, Xiao S, Zhou X, Li H, Wang B, Wei B, Liang H. Stacking modular DNA circuitry in cascading self-assembly of spherical nucleic acids. J Mater Chem B 2017; 5:6256-6265. [DOI: 10.1039/c7tb01307h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Integrated circuitries are successfully built through using the cascaded modular strategy with the assistance of stochastic simulations.
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Affiliation(s)
- Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Hui Li
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at the Microscale
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
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33
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Akiyama Y, Wang G, Shiraishi S, Kanayama N, Takarada T, Maeda M. Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles. ChemistryOpen 2016; 5:508-512. [PMID: 28032016 PMCID: PMC5167314 DOI: 10.1002/open.201600110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 12/25/2022] Open
Abstract
Involvement of single-nucleotide polymorphism (SNP) genotyping in healthcare should allow for more effective use of pharmacogenomics. However, user-friendly assays without the requirement of a special instrument still remain unavailable. This study describes naked-eye SNP discrimination in exon 5 of the human cytochrome P450 2C19 monooxygenase gene, CYP2C19*1 (the wild-type allele) and CYP2C19*2 (the variant allele with G681A point mutation). The present assay is composed of allele-specific single-base primer extension and salt-induced aggregation of DNA-modified gold nanoparticles (DNA-AuNPs). Genetic samples extracted from human hair roots are subjected to this assay. The results are verified by direct sequencing. This study should promise the prospective use of DNA-AuNPs in gene diagnosis.
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Affiliation(s)
- Yoshitsugu Akiyama
- Bioengineering LaboratoryRIKEN2-1 Hirosawa, WakoSaitama351-0198Japan
- Faculty of Industrial Science and TechnologyTokyo University of Science102-1 Tomino, Oshamambe-cho, Yamakoshi-gunHokkaido049-3514Japan
| | - Guoqing Wang
- Bioengineering LaboratoryRIKEN2-1 Hirosawa, WakoSaitama351-0198Japan
| | - Shota Shiraishi
- Bioengineering LaboratoryRIKEN2-1 Hirosawa, WakoSaitama351-0198Japan
| | - Naoki Kanayama
- Bioengineering LaboratoryRIKEN2-1 Hirosawa, WakoSaitama351-0198Japan
- Interdisciplinary Graduate School of Science and TechnologyShinshu University4-7-1 Wakasato, Nagano-shiNagano380-8553Japan
| | - Tohru Takarada
- Bioengineering LaboratoryRIKEN2-1 Hirosawa, WakoSaitama351-0198Japan
| | - Mizuo Maeda
- Bioengineering LaboratoryRIKEN2-1 Hirosawa, WakoSaitama351-0198Japan
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34
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Oishi M, Sugiyama S. An Efficient Particle-Based DNA Circuit System: Catalytic Disassembly of DNA/PEG-Modified Gold Nanoparticle-Magnetic Bead Composites for Colorimetric Detection of miRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5153-5158. [PMID: 27483209 DOI: 10.1002/smll.201601741] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/27/2016] [Indexed: 05/07/2023]
Abstract
An efficient particle-based DNA circuit system for a new colorimetric miRNA assay is designed and devised based on a catalytic disassembly strategy through a target miRNA-triggered DNA circuit mechanism. The new particle-based DNA circuit system shows a rapid color change as well as significant improvement of sensitivity without need for other enzymes or instruments.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan.
| | - Satomi Sugiyama
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan
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35
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Wang G, Akiyama Y, Shiraishi S, Kanayama N, Takarada T, Maeda M. Cross-Linking versus Non-Cross-Linking Aggregation of Gold Nanoparticles Induced by DNA Hybridization: A Comparison of the Rapidity of Solution Color Change. Bioconjug Chem 2016; 28:270-277. [DOI: 10.1021/acs.bioconjchem.6b00410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqing Wang
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshitsugu Akiyama
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shota Shiraishi
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Kanayama
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tohru Takarada
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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36
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Sun P, Ran X, Liu C, Liu C, Pu F, Ren J, Qu X. DNA-fueled molecular machine for label-free and non-enzymatic ultrasensitive detection of telomerase activity. Analyst 2016; 141:4855-8. [PMID: 27405851 DOI: 10.1039/c6an00997b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Herein, a non-enzymatic and label-free strategy based on DNA-fueled molecular machine was developed for ultrasensitive detection of telomerase activity in cancer cell extracts even at the single-cell level.
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Affiliation(s)
- Panpan Sun
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiang Ran
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chaoying Liu
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Fang Pu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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37
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Yao D, Li H, Guo Y, Zhou X, Xiao S, Liang H. A pH-responsive DNA nanomachine-controlled catalytic assembly of gold nanoparticles. Chem Commun (Camb) 2016; 52:7556-9. [PMID: 27225943 DOI: 10.1039/c6cc03089k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The toehold-mediated DNA-strand-displacement reaction has unique programmable properties for driving the catalytic assembly of gold nanoparticles (AuNPs). Herein, we introduced a pH-responsive triplex structure into the DNA-strand-displacement-based catalytic assembly system of DNA-AuNPs to add an additional controlling factor, namely the pH. In this catalytic system, the aggregation rate of AuNPs could be regulated by both internal factors (concentrations of substrate, target, etc.) and an external control (pH gradient). This strategy can be used to construct pH-induced DNA logic gates and sophisticated DNA networks as well as to image instantaneous pH changes in living cells.
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Affiliation(s)
- Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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38
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Chen J, Wen J, Zhuang L, Zhou S. An enzyme-free catalytic DNA circuit for amplified detection of aflatoxin B1 using gold nanoparticles as colorimetric indicators. NANOSCALE 2016; 8:9791-9797. [PMID: 27119550 DOI: 10.1039/c6nr01381c] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An enzyme-free biosensor for the amplified detection of aflatoxin B1 has been constructed based on a catalytic DNA circuit. Three biotinylated hairpin DNA probes (H1, H2, and H3) were designed as the assembly components to construct the sensing system (triplex H1-H2-H3 product). Cascaded signal amplification capability was obtained through toehold-mediated strand displacement reactions to open the hairpins and recycle the trigger DNA. By the use of streptavidin-functionalized gold nanoparticles as the signal indicators, the colorimetric readout can be observed by the naked eye. In the presence of a target, the individual nanoparticles (red) aggregate into a cross-linked network of nanoparticles (blue) via biotin-streptavidin coupling. The colorimetric assay is ultrasensitive, enabling the visual detection of trace levels of aflatoxin B1 (AFB1) as low as 10 pM without instrumentation. The calculated limit of detection (LOD) is 2 pM in terms of 3 times standard deviation over the blank response. The sensor is robust and works even when challenged with complex sample matrices such as rice samples. Our sensing platform is simple and convenient in operation, requiring only the mixing of several solutions at room temperature to achieve visible and intuitive results, and holds great promise for the point-of-use monitoring of AFB1 in environmental and food samples.
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Affiliation(s)
- Junhua Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China.
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39
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Shi K, Dou B, Yang J, Yuan R, Xiang Y. Cascaded strand displacement for non-enzymatic target recycling amplification and label-free electronic detection of microRNA from tumor cells. Anal Chim Acta 2016; 916:1-7. [DOI: 10.1016/j.aca.2016.02.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 12/28/2022]
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40
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Implementing a two-layer feed-forward catalytic DNA circuit for enzyme-free and colorimetric detection of nucleic acids. Anal Chim Acta 2016; 910:68-74. [DOI: 10.1016/j.aca.2016.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/02/2016] [Accepted: 01/07/2016] [Indexed: 12/25/2022]
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41
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Label-free DNA Y junction for bisphenol A monitoring using exonuclease III-based signal protection strategy. Biosens Bioelectron 2016; 77:277-83. [DOI: 10.1016/j.bios.2015.09.042] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/20/2022]
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42
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Huang J, Wang Z, Kim JK, Su X, Li Z. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide. Anal Chem 2015; 87:12254-61. [DOI: 10.1021/acs.analchem.5b03369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiahao Huang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhenyu Wang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jang-Kyo Kim
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public
Health and Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong
| | - Zhigang Li
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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43
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Yao D, Song T, Sun X, Xiao S, Huang F, Liang H. Integrating DNA-Strand-Displacement Circuitry with Self-Assembly of Spherical Nucleic Acids. J Am Chem Soc 2015; 137:14107-13. [DOI: 10.1021/jacs.5b07453] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM
(Collaborative
Innovation Center of Chemistry for Energy Materials), Department of
Polymer Science and Engineering, and ‡Hefei National Laboratory for Physical
Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry, iChEM
(Collaborative
Innovation Center of Chemistry for Energy Materials), Department of
Polymer Science and Engineering, and ‡Hefei National Laboratory for Physical
Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xianbao Sun
- CAS Key Laboratory of Soft Matter Chemistry, iChEM
(Collaborative
Innovation Center of Chemistry for Energy Materials), Department of
Polymer Science and Engineering, and ‡Hefei National Laboratory for Physical
Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM
(Collaborative
Innovation Center of Chemistry for Energy Materials), Department of
Polymer Science and Engineering, and ‡Hefei National Laboratory for Physical
Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Fujian Huang
- CAS Key Laboratory of Soft Matter Chemistry, iChEM
(Collaborative
Innovation Center of Chemistry for Energy Materials), Department of
Polymer Science and Engineering, and ‡Hefei National Laboratory for Physical
Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, iChEM
(Collaborative
Innovation Center of Chemistry for Energy Materials), Department of
Polymer Science and Engineering, and ‡Hefei National Laboratory for Physical
Sciences at the Microscale, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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44
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Shi K, Dou B, Yang C, Chai Y, Yuan R, Xiang Y. DNA-Fueled Molecular Machine Enables Enzyme-Free Target Recycling Amplification for Electronic Detection of MicroRNA from Cancer Cells with Highly Minimized Background Noise. Anal Chem 2015; 87:8578-83. [DOI: 10.1021/acs.analchem.5b02418] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kai Shi
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Baoting Dou
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Cuiyun Yang
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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45
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Yao D, Wang B, Xiao S, Song T, Huang F, Liang H. What Controls the "Off/On Switch" in the Toehold-Mediated Strand Displacement Reaction on DNA Conjugated Gold Nanoparticles? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:7055-7061. [PMID: 26057346 DOI: 10.1021/acs.langmuir.5b01671] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In DNA dynamic nanotechnology, a toehold-mediated DNA strand-displacement reaction has demonstrated its capability in building complex autonomous system. In most cases, the reaction is performed in pure DNA solution that is essentially a one-phase system. In the present work, we systematically investigated the reaction in a heterogeneous media, in which the strand that implements a displacing action is conjugated on gold nanoparticles. By monitoring the kinetics of spherical nucleic acid (SNA) assembly driven by toehold-mediated strand displacement reaction, we observed significant differences, i.e., the abrupt jump in behavior of an "off/on switch", in the reaction rate when the invading toehold was extended to eight bases from seven bases. These phenomena are attributed to the effect of steric hindrance arising from the high density of invading strand conjugated to AuNPs. Based on these studies, an INHIBIT logic gate presenting good selectivity was developed.
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Affiliation(s)
- Dongbao Yao
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Bei Wang
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shiyan Xiao
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Tingjie Song
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Fujian Huang
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Haojun Liang
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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46
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DNA-Encoded Tuning of Geometric and Plasmonic Properties of Nanoparticles Growing from Gold Nanorod Seeds. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500838] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Song T, Tang L, Tan LH, Wang X, Satyavolu NSR, Xing H, Wang Z, Li J, Liang H, Lu Y. DNA-Encoded Tuning of Geometric and Plasmonic Properties of Nanoparticles Growing from Gold Nanorod Seeds. Angew Chem Int Ed Engl 2015; 54:8114-8. [DOI: 10.1002/anie.201500838] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/03/2015] [Indexed: 01/12/2023]
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48
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Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA. Sci Rep 2015; 5:8721. [PMID: 25735213 PMCID: PMC4348642 DOI: 10.1038/srep08721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/23/2015] [Indexed: 12/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.
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49
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Chen J, Wen J, Yang G, Zhou S. A target-induced three-way G-quadruplex junction for 17β-estradiol monitoring with a naked-eye readout. Chem Commun (Camb) 2015; 51:12373-6. [DOI: 10.1039/c5cc04347f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A three-way G-quadruplex junction for 17β-estradiol monitoring has been constructed based on split G-quadruplex DNAzyme and toehold-mediated strand displacement.
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Affiliation(s)
- Junhua Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control
- Guangdong Institute of Eco-Environmental and Soil Sciences
- Guangzhou 510650
- China
| | - Junlin Wen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control
- Guangdong Institute of Eco-Environmental and Soil Sciences
- Guangzhou 510650
- China
| | - Guiqin Yang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control
- Guangdong Institute of Eco-Environmental and Soil Sciences
- Guangzhou 510650
- China
| | - Shungui Zhou
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control
- Guangdong Institute of Eco-Environmental and Soil Sciences
- Guangzhou 510650
- China
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Li H, Xiao S, Yao D, Lam MHW, Liang H. A smart DNA–gold nanoparticle probe for detecting single-base changes on the platform of a quartz crystal microbalance. Chem Commun (Camb) 2015; 51:4670-3. [DOI: 10.1039/c4cc10114f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A design of DNA–gold nanoparticle probe-fueled DNA strand displacements for detecting single-base changes on the platform of a quartz crystal microbalance with random sequences was developed.
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Affiliation(s)
- Hui Li
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
- China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
- China
| | - Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
- China
| | | | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
- China
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