51
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Luo L, Li W, Xiang D, Ma Y, Zhou Y, Xu Y, Chen N, Wang Q, Huang J, Liu J, Yang X, Wang K. Sensitive and specific detection of tumour cells based on a multivalent DNA nanocreeper and a multiplexed fluorescence supersandwich. Chem Commun (Camb) 2020; 56:3693-3696. [PMID: 32123883 DOI: 10.1039/c9cc08618h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A self-assembled DNA nanostructure based on a DNA nanocreeper and multiplexed fluorescence supersandwich was designed for the sensitive and specific detection of tumour cells. This nanostructure could improve the binding affinity of current aptamers and trigger signal amplification, which provide potential for the discrimination of low abundant target cells in liquid biopsy.
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Affiliation(s)
- Lei Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China.
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52
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Wang R, Zhu X, Xing Y, Memon AG, Shi H, Zhou X. Multitag-Regulated Cascade Reaction: A Generalizable Ultrasensitive MicroRNA Biosensing Approach for Cancer Prognosis. ACS APPLIED MATERIALS & INTERFACES 2019; 11:36444-36448. [PMID: 31525882 DOI: 10.1021/acsami.9b14452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ultrasensitive PCR-free microRNA (miR) analysis based on biosensors with enzyme-free nucleic acid amplification and reusable surface has great clinical significance in cancer prognosis. However, building such a biosensing strategy has long been challenging due to uncontrollable miR-triggered cascade amplifiers and insufficient sensing surface regeneration capability. To meet the challenge, for the first time, a general approach, named enzyme-free multitag-regulated cascade reaction (MCR), is developed to fabricate reliable trace miR biosensors. As a proof of concept, miR let-7a is detected on an evanescent wave fluorescent optical-fiber biosensing platform. The size and morphology of well-formed MCR assemblies (∼1 μm in length) are characterized by atomic force microscopy. This MCR method achieves a 30 000-fold improved sensitivity (detection limit 0.8 fM) compared to the MCR-free system and can detect abnormal urinary miR levels in lung cancer patients. Moreover, the biosensor is robust enough to be reused for over 100 cycles, which greatly reduces the cost of single detection. In sum, MCR is developed as a generalizable ultrasensitive miR biosensing approach for cancer prognosis, which opens a broad field for facile enzyme-free biosensing applications by nucleic acid assembling regulation.
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Affiliation(s)
- Ruoyu Wang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Xiyu Zhu
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Yunpeng Xing
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Abdul Ghaffar Memon
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Hanchang Shi
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
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53
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Wang J, Wang DX, Ma JY, Wang YX, Kong DM. Three-dimensional DNA nanostructures to improve the hyperbranched hybridization chain reaction. Chem Sci 2019; 10:9758-9767. [PMID: 32055345 PMCID: PMC6993746 DOI: 10.1039/c9sc02281c] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/29/2019] [Indexed: 11/21/2022] Open
Abstract
Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers.
Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers. However, the traditional HCR occurs through random diffusion of DNA hairpins, making the kinetics and efficiency quite low. By assembling DNA hairpins at the vertexes of tetrahedral DNA nanostructures (TDNs), the reaction kinetics of the HCR is greatly accelerated due to the synergetic contributions of multiple reaction orientations, increased collision probability and enhanced local concentrations. The proposed quadrivalent TDN (qTDN)-mediated hyperbranched HCR has a ∼70-fold faster reaction rate than the traditional HCR. The approximately 76% fluorescence resonance energy transfer (FRET) efficiency obtained is the highest in the reported DNA-based FRET sensing systems as far as we know. Moreover, qTDNs modified by hairpins can easily load drugs, freely traverse plasma membranes and be rapidly cross-linked via the target-triggered HCR in live cells. The reduced freedom of movement as a result of the large crosslinked structure might constrain the hyperbranched HCR in a confined environment, thus making it a promising candidate for in situ imaging and photodynamic therapy. Hence, we present a paradigm of perfect integration of DNA nanotechnology with nucleic acid amplification, thus paving a promising way to the improved performance of nucleic acid amplification techniques and their wider application.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China . .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
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54
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Fabry MH, Ciabrelli F, Munafò M, Eastwood EL, Kneuss E, Falciatori I, Falconio FA, Hannon GJ, Czech B. piRNA-guided co-transcriptional silencing coopts nuclear export factors. eLife 2019; 8:e47999. [PMID: 31219034 PMCID: PMC6677536 DOI: 10.7554/elife.47999] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway is a small RNA-based immune system that controls the expression of transposons and maintains genome integrity in animal gonads. In Drosophila, piRNA-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi. This depends on Panoramix (Panx); however, precisely how an RNA binding event silences transcription remains to be determined. Here we show that Nuclear Export Factor 2 (Nxf2) and its co-factor, Nxt1, form a complex with Panx and are required for co-transcriptional silencing of transposons in somatic and germline cells of the ovary. Tethering of Nxf2 or Nxt1 to RNA results in silencing of target loci and the concomitant accumulation of repressive chromatin marks. Nxf2 and Panx proteins are mutually required for proper localization and stability. We mapped the protein domains crucial for the Nxf2/Panx complex formation and show that the amino-terminal portion of Panx is sufficient to induce transcriptional silencing.
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Affiliation(s)
- Martin H Fabry
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Filippo Ciabrelli
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Ilaria Falciatori
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Federica A Falconio
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
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55
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Karunanayake Mudiyanselage APKK, Wu R, Leon-Duque MA, Ren K, You M. "Second-generation" fluorogenic RNA-based sensors. Methods 2019; 161:24-34. [PMID: 30660865 PMCID: PMC6589113 DOI: 10.1016/j.ymeth.2019.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 02/07/2023] Open
Abstract
A fluorogenic aptamer can specifically interact with a fluorophore to activate its fluorescence. These nucleic acid-based fluorogenic modules have been dramatically developed over the past decade, and have been used as versatile reporters in the sensor development and for intracellular imaging. In this review, we summarize the design principles, applications, and challenges of the first-generation fluorogenic RNA-based sensors. Moreover, we discuss some strategies to develop next-generation biosensors with improved sensitivity, selectivity, quantification property, and eukaryotic robustness. Using genetically encoded catalytic hairpin assembly strategy as an example, we further introduce a standard protocol to design, characterize, and apply these fluorogenic RNA-based sensors for in vitro detection and cellular imaging of target biomolecules. By incorporating natural RNA machineries, nucleic acid nanotechnology, and systematic evolution approaches, next-generation fluorogenic RNA-based devices can be potentially engineered to be widely applied in cell biology and biomedicine.
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Affiliation(s)
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mark A Leon-Duque
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA.
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56
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Sakamoto T, Yamada R. Label‐Free in Situ Monitoring of the DNA Hybridization Chain Reaction by Using Sequence‐Selective Minor‐Groove‐Binding Fluorophores. Chembiochem 2019; 20:1242-1245. [DOI: 10.1002/cbic.201800738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems EngineeringWakayama University 930 Sakaedani Wakayama 640-8510 Japan
| | - Rikuto Yamada
- Faculty of Systems EngineeringWakayama University 930 Sakaedani Wakayama 640-8510 Japan
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57
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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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58
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Chen J, Huang Z, Luo Z, Yu Q, Xu Y, Wang X, Li Y, Duan Y. Multichannel-Structured Three-Dimensional Chip for Highly Sensitive Pathogenic Bacteria Detection Based on Fast DNA-Programmed Signal Polymerization. Anal Chem 2018; 90:12019-12026. [DOI: 10.1021/acs.analchem.8b02650] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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59
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Engelen W, Wijnands SPW, Merkx M. Accelerating DNA-Based Computing on a Supramolecular Polymer. J Am Chem Soc 2018; 140:9758-9767. [PMID: 29989400 PMCID: PMC6077772 DOI: 10.1021/jacs.8b06146] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Dynamic
DNA-based circuits represent versatile systems to perform
complex computing operations at the molecular level. However, the
majority of DNA circuits relies on freely diffusing reactants, which
slows down their rate of operation substantially. Here we introduce
the use of DNA-functionalized benzene-1,3,5-tricarboxamide (BTA) supramolecular
polymers as dynamic scaffolds to template DNA-based molecular computing.
By selectively recruiting DNA circuit components to a supramolecular
BTA polymer functionalized with 10-nucleotide handle strands, the
kinetics of strand displacement and strand exchange reactions were
accelerated 100-fold. In addition, strand exchange reactions were
also favored thermodynamically by bivalent interactions between the
reaction product and the supramolecular polymer. The noncovalent assembly
of the supramolecular polymers enabled straightforward optimization
of the polymer composition to best suit various applications. The
ability of supramolecular BTA polymers to increase the efficiency
of DNA-based computing was demonstrated for three well-known and practically
important DNA-computing operations: multi-input AND gates, Catalytic
Hairpin Assembly and Hybridization Chain Reactions. This work thus
establishes supramolecular BTA polymers as an efficient platform for
DNA-based molecular operations, paving the way for the construction
of autonomous bionanomolecular systems that confine and combine molecular
sensing, computation, and actuation.
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Affiliation(s)
- Wouter Engelen
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Sjors P W Wijnands
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Maarten Merkx
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
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60
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Lanier LA, Bermudez H. Living Supramolecular Polymerization of DNA. Macromol Rapid Commun 2018; 39:e1800342. [PMID: 29974538 DOI: 10.1002/marc.201800342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/31/2018] [Indexed: 01/12/2023]
Abstract
Recently there have been notable synthetic successes in supramolecular polymerization. By contrast, it has long been known that DNA can undergo supramolecular polymerization (concatemerization). Concatemerization is a step-like polymerization and consequently suffers from broad molecular weight distributions and generally undesirable cyclization reactions. Here we demonstrate that another supramolecular polymerization of DNA, hybridization chain reaction (HCR), is in fact a living polymerization. After consumption of initial monomer, the polymerization can be continued with further addition of monomer, and the molecular weight can be varied by the ratio of monomer to initiator. In contrast to concatemerization, HCR produces polymers with narrow dispersity while avoiding cyclization. Identification of the living character of this supramolecular polymerization presents new opportunities in structural DNA nanotechnology and molecular biology.
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Affiliation(s)
- Laura A Lanier
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, 120 Governors Dr, Amherst, MA, 01003, USA
| | - Harry Bermudez
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, 120 Governors Dr, Amherst, MA, 01003, USA
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61
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Ang YS, Li JJ, Chua PJ, Ng CT, Bay BH, Yung LYL. Localized Visualization and Autonomous Detection of Cell Surface Receptor Clusters Using DNA Proximity Circuit. Anal Chem 2018; 90:6193-6198. [PMID: 29608843 DOI: 10.1021/acs.analchem.8b00722] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cell surface receptors play an important role in mediating cell communication and are used as disease biomarkers and therapeutic targets. We present a one-pot molecular toolbox, which we term the split proximity circuit (SPC), for the autonomous detection and visualization of cell surface receptor clusters. Detection was powered by antibody recognition and a series of autonomous DNA hybridization to achieve localized, enzyme-free signal amplification. The system under study was the human epidermal growth factor receptor (HER) family, that is, HER2:HER2 homodimer and HER2:HER3 heterodimer, both in cell lysate and in situ on fixed whole cells. The detection and imaging of receptors were carried out using standard microplate scans and confocal microscopy, respectively. The circuit operated specifically with minimal leakages and successfully captured the receptor expression profiles on three cell types without any intermediate washing steps.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical and Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore
| | - Jia'En Jasmine Li
- Department of Chemical and Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore
| | - Pei-Jou Chua
- Department of Anatomy, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117594 , Singapore
| | - Cheng-Teng Ng
- Department of Anatomy, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117594 , Singapore
| | - Boon-Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117594 , Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical and Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore
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62
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Abstract
DNA biosensors could overcome some of the common drawbacks of lab-based techniques for nucleic acids detection for diagnostics purposes. One of the main impediments for such applications of DNA biosensors is their lack of sensitivity: this can prevent their full exploitation in the diagnostic analytical field. DNA nanotechnology could enhance DNA biosensors and let them perform at the required high sensitivity. Well-designed, programmable self-assembly reactions can be triggered by a specific nucleic acid target. The Hybridization Chain Reaction (HCR) is a self-assembly strategy in which the target nucleic acid sequence triggers the formation of long nicked double-stranded DNA nanostructures. This can be performed in solution or on a surface, and the process can be coupled to different signal transduction schemes. We here describe the methods to design and test HCR reactions for the detection of different nucleic acid targets in solution and the procedures to exploit this strategy on surfaces with an electrochemical biosensing platform.
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Affiliation(s)
- Andrea Miti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giampaolo Zuccheri
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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63
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Liao X, Li Z, Peng T, Li J, Qin F, Huang Z. Ultra-sensitive fluorescent sensor for intracellular miRNA based on enzyme-free signal amplification with carbon nitride nanosheet as a carrier. LUMINESCENCE 2017; 32:1411-1416. [DOI: 10.1002/bio.3338] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/17/2017] [Accepted: 03/26/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Xianjiu Liao
- School of Pharmacy; Youjiang Medical University for Nationalities; Baise Guangxi People's Republic of China
| | - Zhenzhong Li
- School of Pharmacy; Youjiang Medical University for Nationalities; Baise Guangxi People's Republic of China
| | - Tingting Peng
- School of Laboratory Medicine; Youjiang Medical University for Nationalities; Baise Guangxi People's Republic of China
| | - Jie Li
- School of Laboratory Medicine; Youjiang Medical University for Nationalities; Baise Guangxi People's Republic of China
| | - Fengying Qin
- School of Pharmacy; Youjiang Medical University for Nationalities; Baise Guangxi People's Republic of China
| | - Zuliang Huang
- School of Pharmacy; Youjiang Medical University for Nationalities; Baise Guangxi People's Republic of China
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64
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Ying N, Ju C, Li Z, Liu W, Wan J. Visual detection of nucleic acids based on lateral flow biosensor and hybridization chain reaction amplification. Talanta 2017; 164:432-438. [DOI: 10.1016/j.talanta.2016.10.098] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/27/2016] [Accepted: 10/29/2016] [Indexed: 12/21/2022]
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65
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Bi S, Yue S, Zhang S. Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 2017; 46:4281-4298. [DOI: 10.1039/c7cs00055c] [Citation(s) in RCA: 393] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review provides a comprehensive overview of the fundamental principles, analysis techniques, and application fields of hybridization chain reaction and its development status.
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Affiliation(s)
- Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shuzhen Yue
- Collaborative Innovation Center for Marine Biomass Fiber
- Materials and Textiles of Shandong Province
- College of Chemistry and Chemical Engineering
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- Laboratory of Fiber Materials and Modern Textiles
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Makers
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- P. R. China
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66
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Ding X, Cheng W, Li Y, Wu J, Li X, Cheng Q, Ding S. An enzyme-free surface plasmon resonance biosensing strategy for detection of DNA and small molecule based on nonlinear hybridization chain reaction. Biosens Bioelectron 2016; 87:345-351. [PMID: 27587359 DOI: 10.1016/j.bios.2016.08.077] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023]
Abstract
A label-free and enzyme-free surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive and specific detection of target DNA by employing the nonlinear hybridization chain reaction (HCR) amplification. Nonlinear HCR is a hairpin-free system in which double-stranded DNA monomers could dendritically assemble into highly branched nanostructure upon introducing a trigger sequence. The target DNA partly hybridizes with capture probe on the gold sensing chip and the unpaired fragment of target DNA works as a trigger to initiate the nonlinear HCR, forming a chain-branching growth of DNA dendrimer by self-assembly. Real-time amplified SPR response is observed upon the introduction of nonlinear HCR system. The method is capable of detecting target DNA at the concentration down to 0.85 pM in 60min with a dynamic range from 1 pM to 1000 pM, and could discriminate target DNA from mismatched sequences. This biosensing strategy exhibits good reproducibility and precision, and has been successfully applied for detection of target DNA in complex sample matrices. In addition, the nonlinear HCR based SPR biosensing methodology is extended to the detection of adenosine triphosphate (ATP) by aptamer recognition. Thus, the versatile method might become a potential alternative tool for biomolecule detection in medical research and early clinical diagnosis.
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Affiliation(s)
- Xiaojuan Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yujian Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiangling Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xinmin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Quan Cheng
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
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67
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Ang YS, Tong R, Yung LYL. Engineering a robust DNA split proximity circuit with minimized circuit leakage. Nucleic Acids Res 2016; 44:e121. [PMID: 27207880 PMCID: PMC5001597 DOI: 10.1093/nar/gkw447] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/09/2016] [Indexed: 01/17/2023] Open
Abstract
DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically analyzed the sources and characteristics of various types of leakage in a split proximity circuit which was engineered to spatially probe for target sites held within close proximity. Direct evidence that 3′-truncated oligonucleotides were the major impurity contributing to circuit leakage was presented. More importantly, a unique strategy of translocating a single nucleotide between domains, termed ‘inter-domain bridging’, was introduced to eliminate toehold-independent leakages while enhancing the strand displacement kinetics across a three-way junction. We also analyzed the dynamics of intermediate complexes involved in the circuit computation in order to define the working range of domain lengths for the reporter toehold and association region respectively. The final circuit design was successfully implemented on a model streptavidin-biotin system and demonstrated to be robust against both circuit leakage and biological interferences. We anticipate that this simple signal transduction strategy can be used to probe for diverse biomolecular interactions when used in conjunction with specific target recognition moieties.
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Affiliation(s)
- Yan Shan Ang
- Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585
| | - Rachel Tong
- Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585
| | - Lin-Yue Lanry Yung
- Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585
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