1
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Chen J, Fu S, Zhang C, Liu H, Su X. DNA Logic Circuits for Cancer Theranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2108008. [PMID: 35254723 DOI: 10.1002/smll.202108008] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Cancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self-assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor-specific markers and the TME through logic operations and signal amplification, to generate detectable signals or to release anti-cancer agents. In this review, the fundamental concepts of DNA logic circuits are clarified, the basic modules in the circuit are summarized, and how this advanced nano-assembly circuit responds to tumor-related molecules, how to perform logic operations, to realize signal amplification, and selectively release drugs through discussing over 30 application examples, are demonstrated. This review shows that DNA logic circuits have powerful logic judgment and signal amplification functions in improving the specificity and sensitivity of cancer diagnosis and making cancer treatment controllable. In the future, researchers are expected to overcome the existing shortcomings of DNA logic circuits and design smarter DNA devices with better biocompatibility and stability, which will further promote the development of cancer theranostics.
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Affiliation(s)
- Jing Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chunyi Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huiyu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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2
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He JY, Chen ZH, Deng HL, Yuan R, Xu WJ. Antibody-powered DNA switches to initiate the hybridization chain reaction for the amplified fluorescence immunoassay. Analyst 2021; 146:5067-5073. [PMID: 34297024 DOI: 10.1039/d1an01045j] [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
Designing antibody-powered DNA nanodevice switches is crucial and fascinating to perform a variety of functions in response to specific antibodies as regulatory inputs, achieving highly sensitive detection by integration with simple amplified methods. In this work, we report a unique DNA-based conformational switch, powered by a targeted anti-digoxin mouse monoclonal antibody (anti-Dig) as a model, to rationally initiate the hybridization chain reaction (HCR) for enzyme-free signal amplification. As a proof-of-concept, both a fluorophore Cy3-labeled reporter hairpin (RH) in the 3' terminus and a single-stranded helper DNA (HS) were individually hybridized with a recognition single-stranded DNA (RS) modified with Dig hapten, while the unpaired loop of RH was hybridized with the exposed 3'-toehold of HS, isothermally self-assembling an intermediate metastable DNA structure. The introduction of target anti-Dig drove the concurrent conjugation with two tethered Dig haptens, powering the directional switch of this DNA structure into a stable conformation. In this case, the unlocked 3'-stem of RH was implemented to unfold the 5'-stem of the BHQ-2-labeled quench hairpin (QH), rationally initiating the HCR between them by the overlapping complementary hybridization. As a result, numerous pairs of Cy3 and BHQ-2 in the formed long double helix were located in spatial proximity. In response to this, the significant quenching of the fluorescence intensity of Cy3 by BHQ-2 was dependent on the variable concentration of anti-Dig, achieving a highly sensitive quantification down to the picomolar level based on a simplified protocol integrated with enzyme-free amplification.
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Affiliation(s)
- Jia-Yang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ze-Hui Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Hui-Lin Deng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Wen-Ju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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3
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding-upon-Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021; 60:7283-7289. [PMID: 33415794 PMCID: PMC8783695 DOI: 10.1002/anie.202016223] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 09/28/2023]
Abstract
We present a new class of DNA-based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding-upon-repair DNA nanoswitches are synthetic DNA sequences containing O6 -methyl-guanine (O6 -MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation of the O6 -MeG nucleobases they can form stable intramolecular Hoogsteen interactions and fold into an optically active triplex DNA structure. We have first characterized the folding mechanism induced by the enzymatic repair activity through fluorescent experiments and Molecular Dynamics simulations. We then demonstrated that the folding-upon-repair DNA nanoswitches are suitable and specific substrates for different methyltransferase enzymes including the human homologue (hMGMT) and they allow the screening of novel potential methyltransferase inhibitors.
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Affiliation(s)
- Nada Farag
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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4
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nada Farag
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Giulia Palermo
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
- Department of Chemistry University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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5
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Dai Y, Xu W, Somoza RA, Welter JF, Caplan AI, Liu CC. An Integrated Multi‐Function Heterogeneous Biochemical Circuit for High‐Resolution Electrochemistry‐Based Genetic Analysis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yifan Dai
- Electronics Design Center Case Western Reserve University Cleveland OH 44106 USA
- Department of Biomedical Engineering Duke University Durham NC 27708 USA
| | - Wei Xu
- Department of Biomedical Engineering Case Western Reserve University Cleveland OH 44106 USA
| | - Rodrigo A. Somoza
- Department of Biomedical Engineering Case Western Reserve University Cleveland OH 44106 USA
- Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage Department of Biology Case Western Reserve University Cleveland OH 44106 USA
| | - Jean F. Welter
- Department of Biomedical Engineering Case Western Reserve University Cleveland OH 44106 USA
- Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage Department of Biology Case Western Reserve University Cleveland OH 44106 USA
| | - Arnold I. Caplan
- Department of Biomedical Engineering Case Western Reserve University Cleveland OH 44106 USA
- Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage Department of Biology Case Western Reserve University Cleveland OH 44106 USA
| | - Chung Chiun Liu
- Department of Chemical and Biomolecular Engineering Electronics Design Center Case Western Reserve University Cleveland OH 44106 USA
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6
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Dai Y, Xu W, Somoza RA, Welter JF, Caplan AI, Liu CC. An Integrated Multi-Function Heterogeneous Biochemical Circuit for High-Resolution Electrochemistry-Based Genetic Analysis. Angew Chem Int Ed Engl 2020; 59:20545-20551. [PMID: 32835412 PMCID: PMC9306392 DOI: 10.1002/anie.202010648] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 12/22/2022]
Abstract
Modular construction of an autonomous and programmable multi-functional heterogeneous biochemical circuit that can identify, transform, translate, and amplify biological signals into physicochemical signals based on logic design principles can be a powerful means for the development of a variety of biotechnologies. To explore the conceptual validity, we design a CRISPR-array-mediated primer-exchange-reaction-based biochemical circuit cascade, which probes a specific biomolecular input, transform the input into a structurally accessible form for circuit wiring, translate the input information into an arbitrary sequence, and finally amplify the prescribed sequence through autonomous formation of a signaling concatemer. This upstream biochemical circuit is further wired with a downstream electrochemical interface, delivering an integrated bioanalytical platform. We program this platform to directly analyze the genome of SARS-CoV-2 in human cell lysate, demonstrating the capability and the utility of this unique integrated system.
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Affiliation(s)
- Yifan Dai
- Electronics Design Center, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Wei Xu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Rodrigo A Somoza
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
- Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Department of Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jean F Welter
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
- Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Department of Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Arnold I Caplan
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
- Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Department of Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Chung Chiun Liu
- Department of Chemical and Biomolecular Engineering, Electronics Design Center, Case Western Reserve University, Cleveland, OH, 44106, USA
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7
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Dhar A, Ahmed I, Mallick S, Roy S. A Peptide-PNA Hybrid Beacon for Sensitive Detection of Protein Biomarkers in Biological Fluids. Chembiochem 2020; 21:2121-2125. [PMID: 32187425 DOI: 10.1002/cbic.202000097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/14/2020] [Indexed: 01/03/2023]
Abstract
Specific and rapid detection of proteins in biological fluids poses a challenging problem. In biological fluids, many proteins are present at low concentrations, requiring high affinity and specificity of the beacon-protein interaction. We report the design of a peptide-PNA hybrid beacon that exploits the dimeric nature of a target protein, S100B, a biomarker for brain trauma, to enhance binding affinity and specificity. The complementary base-pairing of the PNA bases brings the two arms of the beacon, one carrying an Alexa tag and the other carrying a Dabcyl moiety, into proximity, thus quenching Alexa fluorescence. Each of the arms carries a sequence that binds to one of the subunits. Binding to the target separates the quencher from the probe lifting the quenching of fluorescence. Enhanced affinity and specificity resulting from simultaneously binding to two sites allowed specific detection of S100B at low-nanomolar concentrations in the presence of serum. The design can be easily adapted for the detection of proteins containing multiple binding sites and could prove useful for rapid and sensitive biomarker detection.
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Affiliation(s)
- Amlanjyoti Dhar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Israr Ahmed
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
| | - Shampa Mallick
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
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8
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Hansen-Bruhn M, Nielsen LDF, Gothelf KV. Rapid Detection of Drugs in Human Plasma Using a Small-Molecule-Linked Hybridization Chain Reaction. ACS Sens 2018; 3:1706-1711. [PMID: 30105911 DOI: 10.1021/acssensors.8b00439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Rapid detection and quantification of pharmaceutical drugs directly in human plasma is of major importance for the development of relevant point-of-care testing devices. Here, we report a method for detection and quantification of small molecules in human plasma. An assay employing a small molecule-linked hybridization chain reaction (HCR) has been devised for the detection of the pharmaceutically relevant drugs digoxin (Dig) and methotrexate (MTX). Double modification by small molecule ligands on the initiator strand act as sites to control the rate of the HCR. Upon protein binding to the modified initiator strand, the HCR is greatly inhibited. If the protein is preincubated with a sample containing the small molecule analyte, the protein binding site is occupied by the analyte and the initiator strand will initiate the HCR. This enables efficient detection and quantification of small-molecule analytes in nanomolar concentration even in 50% human plasma within 4 min. Thus, the rapidity and simplicity of this assay has potential for point-of-care testing.
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Affiliation(s)
- Malthe Hansen-Bruhn
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Line D. F. Nielsen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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9
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Shiu SCC, Kinghorn AB, Sakai Y, Cheung YW, Heddle JG, Tanner JA. The Three S's for Aptamer-Mediated Control of DNA Nanostructure Dynamics: Shape, Self-Complementarity, and Spatial Flexibility. Chembiochem 2018; 19:1900-1906. [PMID: 30007003 DOI: 10.1002/cbic.201800308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 01/11/2023]
Abstract
DNA aptamers are ideal tools to enable modular control of the dynamics of DNA nanostructures. For molecular recognition, they have a particular advantage over antibodies in that they can be integrated into DNA nanostructures in a bespoke manner by base pairing or nucleotide extension without any complex bioconjugation strategy. Such simplicity will be critical upon considering advanced therapeutic and diagnostic applications of DNA nanostructures. However, optimizing DNA aptamers for functional control of the dynamics of DNA nanostructure can be challenging. Herein, we present three considerations-shape, self-complementarity, and spatial flexibility-that should be paramount upon optimizing aptamer functionality. These lessons, learnt from the growing number of aptamer-nanostructure reports thus far, will be helpful for future studies in which aptamers are used to control the dynamics of nucleic acid nanostructures.
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Affiliation(s)
- Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yusuke Sakai
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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10
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Harroun SG, Prévost-Tremblay C, Lauzon D, Desrosiers A, Wang X, Pedro L, Vallée-Bélisle A. Programmable DNA switches and their applications. NANOSCALE 2018; 10:4607-4641. [PMID: 29465723 DOI: 10.1039/c7nr07348h] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.
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Affiliation(s)
- Scott G Harroun
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada.
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11
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Guo B, Sheng Y, Zhou K, Liu Q, Liu L, Wu HC. Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yingying Sheng
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Ke Zhou
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Quansheng Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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12
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Guo B, Sheng Y, Zhou K, Liu Q, Liu L, Wu HC. Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing. Angew Chem Int Ed Engl 2018; 57:3602-3606. [PMID: 29488675 DOI: 10.1002/anie.201711690] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/14/2018] [Indexed: 12/26/2022]
Abstract
A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future.
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Affiliation(s)
- Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingying Sheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Ke Zhou
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Quansheng Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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13
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Tian Y, Zhang S, Wang L, Liu S. A Modular Nanoswitch for Mix-and-Detect Protein Assay Based on Binding-Induced Cascade Dissociation of Kissing Complex. Chembiochem 2018; 19:716-722. [PMID: 29356232 DOI: 10.1002/cbic.201700649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Indexed: 01/26/2023]
Abstract
A new modular nanoswitch was described for versatile, rapid (within 1 h), homogeneous, and sensitive protein detection. The system employs two hairpins (HP1 and HP2) that can be reciprocally recognized through the apical loop-loop interaction. HP2 possesses a conformation-switching stem-loop structure, with appended single-stranded tails on each end, which can hybridize with the recognition-element-conjugated DNA strands to construct a protein-responsive HP2 scaffold. It works according to a simple mix-and-detect assay format, with the first formation of a kissing complex between HP1 and HP2 scaffolds for fluorescence quenching, and then cascade propagation from steric strain through protein binding to the dissociation of the kissing complex for fluorescence recovery. The detection universality of such a modular nanoswitch was demonstrated by using three multivalent proteins, including anti-digoxigenin (Anti-Dig) antibody, streptavidin, and thrombin, with detection limits of 0.33, 0.17, and 0.5 nm, respectively.
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Affiliation(s)
- Yishen Tian
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Shanshan Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
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14
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Fabrication of Nanostructures with Bottom-up Approach and Their Utility in Diagnostics, Therapeutics, and Others. ENVIRONMENTAL, CHEMICAL AND MEDICAL SENSORS 2017. [PMCID: PMC7122830 DOI: 10.1007/978-981-10-7751-7_8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanofabrication has been a critical area of research in the last two decades and has found wide-ranging application in improvising material properties, sensitive clinical diagnostics, and detection, improving the efficiency of electron transport processes within materials, generating high energy densities leading to pulse power, novel therapeutic mechanisms, environmental remediation and control. The continued improvements in the various fabrication technologies have led to realization of highly sensitive nanostructure-based devices. The fabrication of nanostructures is in principle carried out primarily using top-down or bottom-up approaches. This chapter summarizes the important bottom-up nanofabrication processes for realizing nanostructures and also highlights the recent research conducted in the domain of therapeutics and diagnostics.
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15
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Abstract
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.
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Affiliation(s)
- Margherita Di Pisa
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
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16
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Cao J, Wang W, Bo B, Mao X, Wang K, Zhu X. A dual-signal strategy for the solid detection of both small molecules and proteins based on magnetic separation and highly fluorescent copper nanoclusters. Biosens Bioelectron 2016; 90:534-541. [PMID: 27825879 DOI: 10.1016/j.bios.2016.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 10/06/2016] [Indexed: 11/28/2022]
Abstract
Recently, a variety of analytical methods for the detection of small molecules or proteins based on small molecule-protein interaction have been developed. However, these methods often focus on either small molecules or proteins. Few efforts are made to detect both of them in the same system. In this work, a dual-signal strategy for the solid detection of both small molecules and proteins based on small molecule-protein interaction is proposed by using the streptavidin-biotin couple as a model. In our strategy, magnetic nanoparticles (MNPs) are adopted for target separation, and highly fluorescent copper nanoclusters (CuNCs) are synthesized in situ to give signals. In the absence of the targets, CuNCs are associated with the MNPs and present in the precipitate under magnetic field; whereas in the presence of either streptavidin or biotin, the CuNCs will present in the supernate. By monitoring the fluorescent intensity of each, dual-signal can be obtained for the solid detection of either the protein or the small molecule. Results show that sensitive and specific detection of both streptavidin (detection limit: 0.47nM) and biotin (detection limit: 3.1nM) can be achieved. This method can be extended for the detection of other small molecule-protein couples, and thereby has the potential for biomedical and clinical applications.
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Affiliation(s)
- Jiepei Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Wei Wang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Bing Bo
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Xiaoxia Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Keming Wang
- Department of Oncology, The second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China.
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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17
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Lv Y, Wu J, Wu P, Chen YZ, Tan Y, Tan C, Jiang Y. A sensitive polymeric dark quencher-based sensing platform for fluorescence “turn on” detection of proteins. RSC Adv 2016. [DOI: 10.1039/c6ra07310g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A sensing platform consisting of polymeric dark quenchers and oppositely charged probes was constructed for detection of proteins.
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Affiliation(s)
- Ying Lv
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Jiatao Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Pan Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yu Zong Chen
- Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics
- Shenzhen Kivita Innovative Drug Discovery Institute
- Shenzhen 518055
- P. R. China
| | - Ying Tan
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
| | - Chunyan Tan
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
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18
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Peng Y, Li X, Yuan R, Xiang Y. Steric hindrance inhibition of strand displacement for homogeneous and signal-on fluorescence detection of human serum antibodies. Chem Commun (Camb) 2016; 52:12586-12589. [DOI: 10.1039/c6cc06893f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Steric hindrance inhibition of strand displacement enables homogeneous and signal-on fluorescence detection of human serum antibodies.
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Affiliation(s)
- Ying Peng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Xin Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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