1
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Volek M, Kurfürst J, Drexler M, Svoboda M, Srb P, Veverka V, Curtis E. Aurora: a fluorescent deoxyribozyme for high-throughput screening. Nucleic Acids Res 2024; 52:9049-9061. [PMID: 38860424 PMCID: PMC11347150 DOI: 10.1093/nar/gkae467] [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] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Fluorescence facilitates the detection, visualization, and tracking of molecules with high sensitivity and specificity. A functional DNA molecule that generates a robust fluorescent signal would offer significant advantages for many applications compared to intrinsically fluorescent proteins, which are expensive and labor intensive to synthesize, and fluorescent RNA aptamers, which are unstable under most conditions. Here, we describe a novel deoxyriboyzme that rapidly and efficiently generates a stable fluorescent product using a readily available coumarin substrate. An engineered version can detect picomolar concentrations of ribonucleases in a simple homogenous assay, and was used to rapidly identify novel inhibitors of the SARS-CoV-2 ribonuclease Nsp15 in a high-throughput screen. Our work adds an important new component to the toolkit of functional DNA parts, and also demonstrates how catalytic DNA motifs can be used to solve real-world problems.
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Affiliation(s)
- Martin Volek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Jaroslav Kurfürst
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Matúš Drexler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Michal Svoboda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 128 44, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
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2
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Hachigian T, Lysne D, Graugnard E, Lee J. Targeted Selection of Aptamer Complementary Elements toward Rapid Development of Aptamer Transducers. J Phys Chem B 2023; 127:4470-4479. [PMID: 37191170 DOI: 10.1021/acs.jpcb.3c01411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Biosensing using aptamers has been a recent interest for their versatility in detecting many different analytes across a wide range of applications, including medical and environmental applications. In our last work, we introduced a customizable aptamer transducer (AT) that could successfully feed-forward many different output domains to target a variety of reporters and amplification reaction networks. In this paper, we explore the kinetic behavior and performance of novel ATs by modifying the aptamer complementary element (ACE) chosen based on a technique for exploring the ligand-binding landscape of duplexed aptamers. Using published data, we selected and constructed several modified ATs that contain ACEs with varying length, position of the start sites, and position of single mismatches, whose kinetic responses were tracked with a simple fluorescence reporter. A kinetic model for ATs was derived and used to extract the strand-displacement reaction constant k1 and the effective aptamer dissociation constant Kd,eff, allowing us to calculate a relative performance metric, k1/Kd,eff. Comparing our results with the predictions based on the literature data, we provide useful insight into the dynamics of the adenosine AT's duplexed aptamer domain and suggest a high-throughput approach for future ATs to be developed with improved sensitivity. The performance of our ATs showed a moderate correlation to those predicted by the ACE scan method. Here, we find that predicted performance based on our ACE selection method was moderately correlated to our AT's performance.
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Affiliation(s)
- Tim Hachigian
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Drew Lysne
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
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3
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Liu W, Samanta A, Deng J, Akintayo CO, Walther A. Mechanistic Insights into the Phase Separation Behavior and Pathway-Directed Information Exchange in all-DNA Droplets. Angew Chem Int Ed Engl 2022; 61:e202208951. [PMID: 36112754 PMCID: PMC9828218 DOI: 10.1002/anie.202208951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Liquid-liquid phase separation provides a versatile approach to fabricating cell-mimicking coacervates. Recently, it was discovered that phase separation of single-stranded DNA (ssDNA) allows for forming protocells and microgels in multicomponent systems. However, the mechanism of the ssDNA phase separation is not comprehensively understood. Here, we present mechanistic insights into the metal-dependent phase separation of ssDNA and leverage this understanding for a straightforward formation of all-DNA droplets. Two phase separation temperatures are found that correspond to the formation of primary nuclei and a growth process. Ca2+ allows for irreversible, whereas Mg2+ leads to reversible phase separation. Capitalizing on these differences makes it possible to control the information transfer of one-component DNA droplets and two-component core-shell protocells. This study introduces new kinetic traps of phase separating ssDNA that lead to new phenomena in cell-mimicking systems.
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Affiliation(s)
- Wei Liu
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Avik Samanta
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Jie Deng
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany,Present address: Department of Cancer BiologyDana-Farber Cancer Institute and Wyss Institute for Biologically Inspired EngineeringHarvard Medical SchoolBostonMA 02115USA
| | - Cecilia Oluwadunsin Akintayo
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany,Cluster of Excellence livMatS @ FIT—Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany,Cluster of Excellence livMatS @ FIT—Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
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4
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Dual-hairpin ligation amplification enabled ultra-sensitive and selective ATP detection for cancer monitor. Biosens Bioelectron 2022; 212:114402. [PMID: 35653851 DOI: 10.1016/j.bios.2022.114402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
Abstract
Abnormal concentration of ATP is related to many diseases such as Parkinson's disease, hypoglycaemia, inflammation and cancer. However, most of the reported strategies exhibit moderate sensitivity with ∼nM level detection limit and few of them can distinguish ATP from its analogues, such as GTP, CTP, UTP and adenosine. Herein, we report an ultra-sensitive and selective ATP detection strategy that combines dual hairpin ligation-induced isothermal amplification (DHLA) with ATP-dependent enzymatic reaction. A good linear relationship between Cq value and ATP concentration in the range from 16 fM to 160 nM is acquired. Meanwhile, the strategy can distinguish ATP from its analogues with high selectivity. Furthermore, our proposed strategy has been successfully utilized to detect ATP from colon cell line and cell culture media with great potential applications in cell metabolism and cancer diagnosis.
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5
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [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
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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6
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Hachigian T, Lysne D, Graugnard E, Lee J. Customizable Aptamer Transducer Network Designed for Feed-Forward Coupling. ACS OMEGA 2021; 6:26888-26896. [PMID: 34693110 PMCID: PMC8529589 DOI: 10.1021/acsomega.1c03146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/24/2021] [Indexed: 05/28/2023]
Abstract
Solution-based biosensors that utilize aptamers have been engineered in a variety of formats to detect a range of analytes for both medical and environmental applications. However, since aptamers have fixed base sequences, incorporation of aptamers into DNA strand displacement networks for feed-forward signal amplification and processing requires significant redesign of downstream DNA reaction networks. We designed a novel aptamer transduction network that releases customizable output domains, which can then be used to initiate downstream strand displacement reaction networks without any sequence redesign of the downstream reaction networks. In our aptamer transducer (AT), aptamer input domains are independent of output domains within the same DNA complex and are reacted with a fuel strand after aptamer-ligand binding. ATs were designed to react with two fluorescent dye-labeled reporter complexes to show the customizability of the output domains, as well as being used as feed-forward inputs to two previously studied catalytic reaction networks, which can be used as amplifiers. Through our study, we show both successful customizability and feed-forward capability of our ATs.
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Affiliation(s)
- Tim Hachigian
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
| | - Drew Lysne
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
| | - Elton Graugnard
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
| | - Jeunghoon Lee
- Micron
School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United
States
- Department
of Chemistry and Biochemistry, Boise State
University, 1910 University
Dr., Boise, Idaho 83725, United States
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7
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Nooranian S, Mohammadinejad A, Mohajeri T, Aleyaghoob G, Kazemi Oskuee R. Biosensors based on aptamer-conjugated gold nanoparticles: A review. Biotechnol Appl Biochem 2021; 69:1517-1534. [PMID: 34269486 DOI: 10.1002/bab.2224] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022]
Abstract
Simply synthetized gold nanoparticles have been highly used in medicine and biotechnology as a result of their biocompatibility, conductivity, and being easily functionalized with biomolecules such as aptamer. Aptamer-conjugated gold nanoparticle structures synergically possess characteristics of both aptamer and gold nanoparticles including high binding affinity, high biocompatibility, enhanced target selectivity, and long circulatory half-life. Aptamer-conjugated gold nanoparticles have extensively gained considerable attention for designing of biosensing systems due to their interesting optical and electrochemical features. Moreover, biosensors based on aptamer-gold nanoparticles are easy to use, with fast response, and inexpensive which make them ideal in individualized medicine, disease markers detection, food safety, and so forth. Moreover, due to high selectivity and biocompatibility of aptamer-gold nanoparticles, these biosensing platforms are ideal tools for targeted drug delivery systems. The application of this nanostructure as diagnostic and therapeutic tool has been developed for detection of cancer in the early stage by detecting cancer biomarkers, pathogens, proteins, toxins, antibiotics, adenosine triphosphate, and other small molecules. This review obviously demonstrates that this nanostructure effectively is applicable in the field of biomedicine and possesses potential of commercialization aims.
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Affiliation(s)
- Samin Nooranian
- Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arash Mohammadinejad
- Targeted Drug Delivery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Taraneh Mohajeri
- Department of Obstetrics & Gynecology, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Ghazaleh Aleyaghoob
- Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kazemi Oskuee
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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8
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Yang H, Peng Y, Xu M, Xu S, Zhou Y. Development of DNA Biosensors Based on DNAzymes and Nucleases. Crit Rev Anal Chem 2021; 53:161-176. [PMID: 34225516 DOI: 10.1080/10408347.2021.1944046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Peng
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Mingming Xu
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Shuxia Xu
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China.,College of Ecology and Environment, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science, Yangtze University, Jingzhou, Hubei, China
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9
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Ju Y, Kim HY, Ahn JK, Park HG. Ultrasensitive version of nucleic acid sequence-based amplification (NASBA) utilizing a nicking and extension chain reaction system. NANOSCALE 2021; 13:10785-10791. [PMID: 34076022 DOI: 10.1039/d1nr00564b] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleic acid sequence-based amplification (NASBA) is a transcription-based isothermal amplification technique especially designed for the detection of RNA targets. The NASBA basically relies on the linear production of T7 RNA promoter-containing double-stranded DNA (T7DNA), and thus the final amplification efficiency is not sufficiently high enough to achieve ultrasensitive detection. We herein ingeniously integrate a nicking and extension chain reaction system into the NASBA to establish an ultrasensitive version of NASBA, termed Nicking and Extension chain reaction System-Based Amplification (NESBA). By employing a NESBA primer set designed to contain an additional nicking site at the 5' end of a NASBA primer set, the T7DNA is exponentially amplified through continuously repeated nicking and extension chain reaction by the combined activities of nicking endonuclease (NE) and reverse transcriptase (RT). As a consequence, a much larger number of RNA amplicons would be produced through the transcription of the amplified T7DNA, greatly enhancing the final fluorescence signal from the molecular beacon (MB) probe binding to the RNA amplicon. Based on this unique design principle, we successfully identified the target respiratory syncytial virus A (RSV A) genomic RNA (gRNA) down to 1 aM under isothermal conditions, which is 100-fold more sensitive than regular NASBA.
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Affiliation(s)
- Yong Ju
- Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jun Ki Ahn
- Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea. and Human Convergence Technology Group, Korea Institute of Industrial Technology (KITECH), 143 Hanggaul-ro, Sangnok-gu, Ansan 15588, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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10
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Xu W, He W, Du Z, Zhu L, Huang K, Lu Y, Luo Y. Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications. Angew Chem Int Ed Engl 2021; 60:6890-6918. [PMID: 31729826 PMCID: PMC9205421 DOI: 10.1002/anie.201909927] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/29/2019] [Indexed: 01/01/2023]
Abstract
Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.
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Affiliation(s)
- Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Wanchong He
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana, Illinois 61801 (USA)
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
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11
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Zhou Z, Zhang Y, Guo M, Huang K, Xu W. Ultrasensitive magnetic DNAzyme-copper nanoclusters fluorescent biosensor with triple amplification for the visual detection of E. coli O157:H7. Biosens Bioelectron 2020; 167:112475. [DOI: 10.1016/j.bios.2020.112475] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/10/2023]
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12
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Xu W, He W, Du Z, Zhu L, Huang K, Lu Y, Luo Y. Funktionelle Nukleinsäure‐Nanomaterialien: Entwicklung, Eigenschaften und Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Wanchong He
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Yi Lu
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
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13
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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14
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Hu Q, Gan S, Bao Y, Zhang Y, Han D, Niu L. Controlled/“living” radical polymerization-based signal amplification strategies for biosensing. J Mater Chem B 2020; 8:3327-3340. [DOI: 10.1039/c9tb02419k] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Controlled/“living” radical polymerization-based signal amplification strategies and their applications in highly sensitive biosensing of clinically relevant biomolecules are reviewed.
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Affiliation(s)
- Qiong Hu
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Shiyu Gan
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Yu Bao
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Yuwei Zhang
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Dongxue Han
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Li Niu
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
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15
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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16
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Qi L, Hu Q, Kang Q, Bi Y, Jiang Y, Yu L. Detection of Biomarkers in Blood Using Liquid Crystals Assisted with Aptamer-Target Recognition Triggered in Situ Rolling Circle Amplification on Magnetic Beads. Anal Chem 2019; 91:11653-11660. [PMID: 31430128 DOI: 10.1021/acs.analchem.9b02186] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of biomarkers in body fluids is critical to both diagnosing the life-threatening diseases and optimizing therapeutic interventions. We herein report use of liquid crystals (LCs) to detect biomarkers in blood with high sensitivity and specificity by employing in situ rolling circle amplification (RCA) on magnetic beads (MBs). Specific recognition of cancer biomarkers, such as platelet derived growth factor BB (PDGF-BB) and adenosine, by aptamers leads to formation of a nucleic acid circle on MBs preassembled with ligation DNA, linear padlock DNA, and aptamers, thereby triggering in situ RCA. LCs change from dark to bright appearance after the in situ RCA products being transferred onto the LC interface decorated with octadecy trimethylammonium bromide (OTAB), which is particularly sensitive to the amplified DNA on MBs. Overall, this label-free approach takes advantages of high specificity of aptamer-based assay, efficient enrichment of signaling molecules on MBs, remarkable DNA elongation performance of the RCA reaction, and high sensitivity of LC-based assay. It successfully eliminates the matrix interference on the LC-based sensors and thus achieves at least 4 orders of magnitude improvement in sensitivity for detection of biomarkers compared to other LC-based sensors. In addition, performance of the developed sensor is comparable to that of the commercial ones. Thus, this study provides a simple, powerful, and promising approach to facilitate highly sensitive, specific, and label-free detection of biomarkers in body fluids.
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Affiliation(s)
- Lubin Qi
- Key Laboratory of Colloid and Interface Chemistry , Shandong University, Ministry of Education , Jinan 250100 , China
| | - Qiongzheng Hu
- Shandong Analysis and Test Center , Qilu University of Technology (Shandong Academy of Sciences) , Jinan 250014 , China
| | - Qi Kang
- College of Chemistry, Chemical Engineering and Materials Science , Shandong Normal University , Jinan 250014 , China
| | - Yanhui Bi
- Key Laboratory of Colloid and Interface Chemistry , Shandong University, Ministry of Education , Jinan 250100 , China
| | - Yifei Jiang
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Li Yu
- Key Laboratory of Colloid and Interface Chemistry , Shandong University, Ministry of Education , Jinan 250100 , China
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17
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Sharafdarkolaee SH, Gill P, Motovali-Bashi M, Sharafdarkolaee FH. Isothermal Amplification Methods for the SNP Genotyping. Curr Mol Med 2019; 19:461-472. [PMID: 31131752 DOI: 10.2174/1566524019666190527083947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/30/2018] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
The demands for genotyping techniques with acceptable precision, accuracy, cost-effectiveness in high throughput formats made driving forces for continuous development of novel technologies. A wide range of mutation detection techniques based on polymerase chain reaction (PCR) have been introduced. The best alternatives were the isothermal amplification technologies that those did not require a thermal cycler. In this review, we aimed to describe the most known isothermal amplification techniques for SNP genotyping.
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Affiliation(s)
| | - Pooria Gill
- Nanomedicine Group, Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Motovali-Bashi
- Department of Genetics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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18
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Li J, Kong C, Liu Q, Chen Z. Colorimetric ultrasensitive detection of DNA based on the intensity of gold nanoparticles with dark-field microscopy. Analyst 2019; 143:4051-4056. [PMID: 30059077 DOI: 10.1039/c8an00825f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present an ultrasensitive colorimetric nucleic acid assay based on the intensity of gold nanoparticles (Au NPs) using dark field microscopy. In the absence of target DNA, two hairpin-like DNA strands with protruding single-stranded DNA (ssDNA) can be absorbed onto the Au NP surface via non-covalent interactions between the exposed nitrogen bases of ssDNA and Au NPs, which inhibits Au NPs from aggregating in a high concentration of salt media, while in the presence of target DNA, two hairpin DNA strands hybridize with target DNA to form double-stranded DNA (dsDNA). After hybridization chain reaction (HCR) amplification, rigid dsDNA polymers are formed, which results in serious Au NP aggregation in the salt environment. By measuring the intensity change of yellow and red dots on a dark-field image, the concentration of target DNA can be accurately quantified with a limit of detection (LOD) of 66 fM.
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Affiliation(s)
- Jingjing Li
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China.
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19
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Teng J, Huang L, Zhang L, Li J, Bai H, Li Y, Ding S, Zhang Y, Cheng W. High-sensitive immunosensing of protein biomarker based on interfacial recognition-induced homogeneous exponential transcription. Anal Chim Acta 2019; 1067:107-114. [PMID: 31047141 DOI: 10.1016/j.aca.2019.03.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/12/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023]
Abstract
A novel and versatile immunosensing strategy was developed for ultrasensitive and specific detection of proteins by organically integrating interfacial specific target recognition and homogeneous transcription amplification. In principle, classic antigen-antibody sandwich structure on the microplate could realize the specific identification of target protein. Biotinylated DNA probe was subsequently introduced by streptavidin-biotin system as a bridge linking interfacial and homogeneous reaction. The biotinylated DNA initiated exponential transcription amplification in the solution, which converted per target recognition event on the interface to numerous single-stranded RNA products in solution for highly sensitive fluorescence immunosensing. The proposed immunoassay based on interfacial recognition-induced homogeneous exponential transcription (IR-HET) for vascular endothelial growth factor (VEGF) detection showed a good linear range from 0.01 to 1000 pg/mL and the limit of detection as low as 1 fg/mL, which was 3 orders lower than traditional ELISA method. The established strategy was also successfully applied to directly detect VEGF from culture supernatants of tumor cells and clinical body fluid samples, proving very high sensitivity, selectivity and low matrix effect. Therefore, IR-HET-based immunosensing strategy might become a potential powerful tool be applied in ultrasensitive detection of low abundance protein biomarker for clinical early diagnosis, treatment and prognosis.
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Affiliation(s)
- Jie Teng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Lizhen Huang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Lutan Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jia Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China; Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Huili Bai
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Ying Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yuhong Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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20
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Wang J, Wang Y, Liu S, Wang H, Zhang X, Song X, Huang J. Duplex featured polymerase-driven concurrent strategy for detecting of ATP based on endonuclease-fueled feedback amplification. Anal Chim Acta 2019; 1060:79-87. [PMID: 30902334 DOI: 10.1016/j.aca.2019.01.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/11/2019] [Accepted: 01/23/2019] [Indexed: 12/24/2022]
Abstract
We have developed a novel amplification strategy termed Endo IV-assisted feedback amplification (EFA) taking advantages of rolling circular amplification (RCA) and Endo IV-assisted signal amplification (ESA) biosensing platform for detecting of adenosine triphosphate (ATP). Two kinds of specially programmed DNA complexes were employed into EFA system, one composed of a split aptamer fragment and a circular template, and the other composed of AP probe and the same circular template. Hence, ATP as a target induced the self-assembly of spilt aptamer fragments and initiated RCA reaction generating a linear DNA, which consists of hybridization elements with Complex II and formation elements of G-quadruplex. More importantly, the addition of endonuclease IV can cut the Complex II into two parts, and one of which can be trimming by phi29 DNA polymerase initiating the new round of RCA reaction producing more RCA products. Thus significantly enhanced fluorescent signal can be measured for ATP as expected, and our proposed strategy exhibits improved performances toward ATP ultrasensitive detection with a limit of detection (LOD) as low as 0.09 nM. Additionally, our developed biosensor demonstrates high selectivity and the superiority of simplicity towards ATP. Above these significant aspects, our proximity binding-induced RCA reaction-based fluorescent assay and Endo IV-fueled feedback signal amplification strategy presents an optimal detection performance towards ATP for potential application in related research and clinical diagnosis.
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Affiliation(s)
- Jingfeng Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Yu Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Su Liu
- College of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Haiwang Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Xue Zhang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Xiaolei Song
- College of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Jiadong Huang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China; Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, College of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.
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21
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Chen J, Baker YR, Brown A, El-Sagheer AH, Brown T. Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation. Chem Sci 2018; 9:8110-8120. [PMID: 30542561 PMCID: PMC6238721 DOI: 10.1039/c8sc02952k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cyclic oligonucleotides are valuable targets with a broad range of potential applications spanning molecular biology and nanotechnology. Of particular importance is their role as templates in the rolling circle amplification (RCA) reaction. We describe three different chemical cyclisation methods for the preparation of single-stranded cyclic DNA constructs. These chemical cyclisation reactions are cheaper to carry out than the enzymatic reaction, and more amenable to preparative scale purification and characterisation of the cyclic product. They can also be performed under denaturing conditions and are therefore particularly valuable for cyclic DNA templates that contain secondary structures. The resulting single-stranded cyclic DNA constructs contain a single non-canonical backbone linkage at the ligation point (triazole, amide or phosphoramidate). They were compared to unmodified cyclic DNA in rolling circle amplification reactions using φ-29 and Bst 2.0 DNA polymerase enzymes. The cyclic templates containing a phosphoramidate linkage were particularly well tolerated by φ-29 polymerase, consistently performing as well in RCA as the unmodified DNA controls. Moreover, these phosphoramidate-modified cyclic constructs can be readily produced in oligonucleotide synthesis facilities from commercially available precursors. Phosphoramidate ligation therefore holds promise as a practical, scalable method for the synthesis of fully biocompatible cyclic RCA templates. The triazole-modified cyclic templates generally gave lower and more variable yields of RCA products, a significant proportion of which were double-stranded, while the performances of the templates containing an amide linkage lie in between those of the phosphoramidate- and triazole-containing templates.
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Affiliation(s)
- Jinfeng Chen
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Ysobel R Baker
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Asha Brown
- ATDBio , Magdalen Centre , Oxford Science Park , Oxford , OX4 4GA , UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
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22
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An electrochemical ceruloplasmin aptasensor using a glassy carbon electrode modified by diazonium-functionalized multiwalled carbon nanotubes. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2018. [DOI: 10.1007/s13738-018-1533-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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23
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Qi H, Yue S, Bi S, Ding C, Song W. Isothermal exponential amplification techniques: From basic principles to applications in electrochemical biosensors. Biosens Bioelectron 2018; 110:207-217. [PMID: 29625328 DOI: 10.1016/j.bios.2018.03.065] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/16/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022]
Abstract
As a conventional amplification technique, polymerase chain reaction (PCR) has been widely applied to detect a variety of analytes with exponential amplification efficiency. However, the requirement of thermocycling procedures largely limits the application of PCR-based methods. Alternatively, several isothermal amplification techniques have been developed since the early 1990s. In particular, according to the reaction kinetics, isothermal exponential amplification techniques possess higher amplification efficiency and detection sensitivity. The isothermal exponential amplification techniques can be mainly divided into two categories: enzyme-based isothermal exponential amplification and enzyme-free isothermal exponential amplification. Considering the advantages of high sensitivity and selectivity, high signal-to-noise ratio, low cost and rapid response time, exponential amplification electrochemical biosensors have attracted considerable attention. In this review, we introduce the basic principles of isothermal exponential amplification techniques and summarize their applications in electrochemical biosensors during the past five years. We also highlighted the present challenges and further perspectives of isothermal exponential amplification-based electrochemical biosensors.
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Affiliation(s)
- Hongjie Qi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Shuzhen Yue
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China
| | - Sai Bi
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, PR China.
| | - Caifeng Ding
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Weiling Song
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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24
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Hede MS, Fjelstrup S, Lötsch F, Zoleko RM, Klicpera A, Groger M, Mischlinger J, Endame L, Veletzky L, Neher R, Simonsen AKW, Petersen E, Mombo-Ngoma G, Stougaard M, Ho YP, Labouriau R, Ramharter M, Knudsen BR. Detection of the Malaria causing Plasmodium Parasite in Saliva from Infected Patients using Topoisomerase I Activity as a Biomarker. Sci Rep 2018. [PMID: 29515150 PMCID: PMC5841400 DOI: 10.1038/s41598-018-22378-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Malaria is among the major threats to global health with the main burden of disease being in rural areas of developing countries where accurate diagnosis based on non-invasive samples is in high demand. We here present a novel molecular assay for detection of malaria parasites based on technology that may be adapted for low-resource settings. Moreover, we demonstrate the exploitation of this assay for detection of malaria in saliva. The setup relies on pump-free microfluidics enabled extraction combined with a DNA sensor substrate that is converted to a single-stranded DNA circle specifically by topoisomerase I expressed by the malaria causing Plasmodium parasite. Subsequent rolling circle amplification of the generated DNA circle in the presence of biotin conjugated deoxynucleotides resulted in long tandem repeat products that was visualized colorimetrically upon binding of horse radish peroxidase (HRP) and addition of 3,3′,5,5′-Tetramethylbenzidine that was converted to a blue colored product by HRP. The assay was directly quantitative, specific for Plasmodium parasites, and allowed detection of Plasmodium infection in a single drop of saliva from 35 out of 35 infected individuals tested. The results could be determined directly by the naked eye and documented by quantifying the color intensity using a standard paper scanner.
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Affiliation(s)
| | - Søren Fjelstrup
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark
| | - Felix Lötsch
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Anna Klicpera
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Mirjam Groger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Johannes Mischlinger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Lilian Endame
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Luzia Veletzky
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Ronja Neher
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | | | - Eskild Petersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Infectious Diseases, The Royal Hospital, Muscat, Oman
| | - Ghyslain Mombo-Ngoma
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Magnus Stougaard
- Department of Clinical Medicine, University of Aarhus, Aarhus, Denmark
| | - Yi-Ping Ho
- Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | | | - Michael Ramharter
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark.
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25
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Zhou H, Liu J, Xu JJ, Zhang SS, Chen HY. Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application. Chem Soc Rev 2018; 47:1996-2019. [PMID: 29446429 DOI: 10.1039/c7cs00573c] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.
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Affiliation(s)
- Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Jing Liu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Jing-Juan Xu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Shu-Sheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Hong-Yuan Chen
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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26
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Yuan D, Ding L, Sun Z, Li X. MRI/Fluorescence bimodal amplification system for cellular GSH detection and tumor cell imaging based on manganese dioxide nanosheet. Sci Rep 2018; 8:1747. [PMID: 29379132 PMCID: PMC5788857 DOI: 10.1038/s41598-018-20110-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/11/2018] [Indexed: 11/22/2022] Open
Abstract
Here, we report a novel magnetic resonance imaging (MRI)/fluorescence bimodal amplification platform for the detection of glutathione (GSH) on the basis of redoxable manganese dioxide (MnO2) nanosheets, which can be readily applied as a DNA nanocarrier, fluorescence quencher, and intracellular GSH-activated MRI contrast agent. The binding of aptamers that absorbed on the MnO2 nanosheets to their target can facilitating the endocytosis of target-nanoprobes. Once endocytosed, the MnO2 nanosheets can react with cellular GSH, resulting in the disintegration of nanosheets to generate plenty of Mn2+ ions for MRI and releases the primers which were adsorbed on the MnO2 nanosheets. Then the rolling circle amplification (RCA) reaction was initiated to amplify the fluorescence signal. In addition, after treatment with GSH, the MnO2 nanosheets were reduced and then most of the fluorescence was recovered. Therefore, this MnO2 nanoprobe exhibits excellent selectivity, suggesting a potential detection platform for analyzing the glutathione level in cells.
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Affiliation(s)
- Dandan Yuan
- Center of Cooperative Innovation for Chemical Imaging Functional Probes in Universities of Shandong, College of Chemistry, Shandong Normal University, Jinan, 250014, P. R. China.,Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Research Institute of Biochemical Analysis, Linyi University, Linyi, 276005, P. R. China
| | - Lairong Ding
- Center of Cooperative Innovation for Chemical Imaging Functional Probes in Universities of Shandong, College of Chemistry, Shandong Normal University, Jinan, 250014, P. R. China.,Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Research Institute of Biochemical Analysis, Linyi University, Linyi, 276005, P. R. China
| | - Zhaomei Sun
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Research Institute of Biochemical Analysis, Linyi University, Linyi, 276005, P. R. China
| | - Xuemei Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Research Institute of Biochemical Analysis, Linyi University, Linyi, 276005, P. R. China.
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27
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Ma F, Liu H, Li CC, Zhang CY. A simple and isothermal ligase-based amplification approach based on a ligation-activated cleavage reaction. Chem Commun (Camb) 2018; 54:12638-12641. [DOI: 10.1039/c8cc07843b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We develop a simple and isothermal ligase-based cyclic amplification approach for the sensitive detection of polynucleotide kinase, DNA, proteins and ATP.
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Affiliation(s)
- Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Huan Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chen-chen Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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28
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Kristoffersen EL, Givskov A, Jørgensen LA, Jensen PW, W Byl JA, Osheroff N, Andersen AH, Stougaard M, Ho YP, Knudsen BR. Interlinked DNA nano-circles for measuring topoisomerase II activity at the level of single decatenation events. Nucleic Acids Res 2017; 45:7855-7869. [PMID: 28541438 PMCID: PMC5570003 DOI: 10.1093/nar/gkx480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/22/2017] [Indexed: 12/23/2022] Open
Abstract
DNA nano-structures present appealing new means for monitoring different molecules. Here, we demonstrate the assembly and utilization of a surface-attached double-stranded DNA catenane composed of two intact interlinked DNA nano-circles for specific and sensitive measurements of the life essential topoisomerase II (Topo II) enzyme activity. Topo II activity was detected via the numeric release of DNA nano-circles, which were visualized at the single-molecule level in a fluorescence microscope upon isothermal amplification and fluorescence labeling. The transition of each enzymatic reaction to a micrometer sized labeled product enabled quantitative detection of Topo II activity at the single decatenation event level rendering activity measurements in extracts from as few as five cells possible. Topo II activity is a suggested predictive marker in cancer therapy and, consequently, the described highly sensitive monitoring of Topo II activity may add considerably to the toolbox of individualized medicine where decisions are based on very sparse samples.
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Affiliation(s)
- Emil L Kristoffersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark
| | - Asger Givskov
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Line A Jørgensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Pia W Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Anni H Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark.,Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark
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29
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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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30
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Shen C, Zeng K, Luo J, Li X, Yang M, Rasooly A. Self-Assembled DNA Generated Electric Current Biosensor for HER2 Analysis. Anal Chem 2017; 89:10264-10269. [PMID: 28859480 DOI: 10.1021/acs.analchem.7b01747] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have developed a new DNA self-assembly amplification technology that generates electric current for electrochemical biosensing. The new technology was used for detection of human epidermal growth factor receptor 2 (HER2). In our technology, an aptamer was utilized both as a ligand for recognition and as a signal generating reporter. The aptasensor is based on a sandwich format and a DNA primer on a HER2 aptamer initiates auxiliary DNA self-assembled on the electrode to form a long one-dimensional DNA. The resulting DNA is then reacted with molybdate to generate electrochemical current. The sensitivity of the aptasensor with DNA self-assembly was greater than that of the aptasensor without DNA self-assembly due to the extended length of the DNA strand. Aptasensor analysis of HER2 in serum of breast cancer patients and healthy individuals is highly correlated (R2 = 0.9924) with ELISA measurements, with a p value of 1.37 × 10-7. The analysis of HER2 in serum (confirmed by ELISA) suggests that HER2 levels in breast cancer patients are much higher than healthy individuals. For HER2 positive patients, the levels are higher than those of HER2 negative patients. After surgery, there is a drop of HER2 levels in serum, suggesting potential clinical applications of the new self-assembled DNA electric current generating biosensor. Unlike proteins, DNA is easily amplifiable. The DNA signal amplification method presented here enables effective current generation, which can find wide range of biomedical applications for protein detection.
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Affiliation(s)
- Congcong Shen
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Ke Zeng
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Junjun Luo
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Xiaoqing Li
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Minghui Yang
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Avraham Rasooly
- National Cancer Institute, National Institutes of Health , Rockville, Maryland 20850, United States
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31
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Shi L, Peng P, Du Y, Li T. Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device. Nucleic Acids Res 2017; 45:4306-4314. [PMID: 28369541 PMCID: PMC5416763 DOI: 10.1093/nar/gkx202] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/18/2017] [Indexed: 01/24/2023] Open
Abstract
Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (Cn-1TmCn and CnTmCn-1; n = 3−6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability. The L-form structures generally display a relatively low stability, with a bigger difference from that of conventional i-motifs formed by CnTmCn. It inspires us to at utmost improving the structural stability by extending the core of L-form bimolecular i-motifs with a few flanking noncanonical base pairs, and therefore to avoid the dimeric association of each component. This meaningful bimolecular i-motif is then incorporated into a three-way junction (3WJ) and a four-way junction (4WJ) functionalized with two components of a ATP-binding split DNA aptamer, allowing the pH-triggered directional assembly of 3WJ and 4WJ into the desired (3+4)WJ structure that is verified by gel electrophoresis. It therefore enables the ATP-induced association of the split aptamer within the (3+4)WJ structure, as monitored by fluorescence quenching. In this way, the designed DNA system behaves as a pH-switched reversible molecular device, showing a high sensitivity and selectivity for fluorescent ATP analysis. The i-motif folding topology-programmed DNA nanoassembly may find more applications in the context of larger 2D/3D DNA nanostructures like lattices and polyhedra.
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Affiliation(s)
- Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yi Du
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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32
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Huang B, Geng Z, Yan S, Li Z, Cai J, Wang Z. Water-Soluble Conjugated Polymer as a Fluorescent Probe for Monitoring Adenosine Triphosphate Level Fluctuation in Cell Membranes during Cell Apoptosis and in Vivo. Anal Chem 2017; 89:8816-8821. [PMID: 28752761 DOI: 10.1021/acs.analchem.7b01212] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Adenosine triphosphate (ATP) is used as the energy source in cells and plays crucial roles in various cellular events. The cellular membrane is the protective barrier for the cytoplasm of living cells and involved in many essential biological processes. Many fluorescent probes for ATP have been successfully developed, but few of these probes were appropriate for visualizing ATP level fluctuation in cell membranes during the apoptotic cell death process. Herein, we report the synthesis of a new water-soluble cationic polythiophene derivative that can be utilized as a fluorescent sensor for detecting ATP in cell membranes. Poly((3-((4-methylthiophen-3-yl)oxy)propyl)triphenylphosphonium chloride) (PMTPP) exhibits high sensitivity and good selectivity to ATP, and the detection limit is 27 nM. The polymer shows low toxicity to live cells and excellent photostability in cell membranes. PMTPP was practically utilized for real-time monitoring of ATP levels in the cell membrane through fluorescence microscopy. We have demonstrated that the ATP levels in cell membranes increased during the apoptotic cell death process. The probe was also capable of imaging ATP levels in living mice.
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Affiliation(s)
- Binghuan Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zhirong Geng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Shihai Yan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zan Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Jun Cai
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zhilin Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
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33
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Shi C, Wang Y, Zhang M, Ma C. DNA Self-assembly Catalyzed by Artificial Agents. Sci Rep 2017; 7:6818. [PMID: 28754968 PMCID: PMC5533707 DOI: 10.1038/s41598-017-07210-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/27/2017] [Indexed: 11/08/2022] Open
Abstract
Nucleic acids have been shown to be versatile molecules and engineered to produce various nanostructures. However, the poor rate of these uncatalyzed nucleic acid reactions has restricted the development and applications. Herein, we reported a novel finding that DNA self-assembly could be nonenzymatically catalyzed by artificial agents with an increasing dissociation rate constant K2. The catalytic role of several artificial agents in DNA self-assembly was verified by real-time fluorescent detection or agarose gel electrophoresis. We found that 20% PEG 200 could significantly catalyze DNA self-assembly and increase the reaction efficiency, such as linear hybridization chain reaction (HCR) and exponential hairpin assembly (EHA). Therefore, we foresee that a fast and efficient DNA self-assembly in structural DNA nanotechnology will be desirable.
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Affiliation(s)
- Chao Shi
- College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Yifan Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China
| | - Menghua Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China
| | - Cuiping Ma
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P.R. China.
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34
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Umesha S, Manukumar HM. Advanced molecular diagnostic techniques for detection of food-borne pathogens: Current applications and future challenges. Crit Rev Food Sci Nutr 2017; 58:84-104. [PMID: 26745757 DOI: 10.1080/10408398.2015.1126701] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The elimination of disease-causing microbes from the food supply is a primary goal and this review deals with the overall techniques available for detection of food-borne pathogens. Now-a-days conventional methods are replaced by advanced methods like Biosensors, Nucleic Acid-based Tests (NAT), and different PCR-based techniques used in molecular biology to identify specific pathogens. Bacillus cereus, Staphylococcus aureus, Proteus vulgaris, Escherichia coli, Campylobacter, Listeria monocytogenes, Salmonella spp., Aspergillus spp., Fusarium spp., Penicillium spp., and pathogens are detected in contaminated food items that cause always diseases in human in any one or the other way. Identification of food-borne pathogens in a short period of time is still a challenge to the scientific field in general and food technology in particular. The low level of food contamination by major pathogens requires specific sensitive detection platforms and the present area of hot research looking forward to new nanomolecular techniques for nanomaterials, make them suitable for the development of assays with high sensitivity, response time, and portability. With the sound of these, we attempt to highlight a comprehensive overview about food-borne pathogen detection by rapid, sensitive, accurate, and cost affordable in situ analytical methods from conventional methods to recent molecular approaches for advanced food and microbiology research.
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Affiliation(s)
- S Umesha
- a Department of Studies in Biotechnology , University of Mysore, Manasagangotri , Mysore , Karnataka , India
| | - H M Manukumar
- a Department of Studies in Biotechnology , University of Mysore, Manasagangotri , Mysore , Karnataka , India
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35
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Zhao J, Lei YM, Chai YQ, Yuan R, Zhuo Y. Novel electrochemiluminescence of perylene derivative and its application to mercury ion detection based on a dual amplification strategy. Biosens Bioelectron 2016; 86:720-727. [DOI: 10.1016/j.bios.2016.07.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 12/30/2022]
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36
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Aptamer based electrochemical adenosine triphosphate assay based on a target-induced dendritic DNA nanoassembly. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-2026-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Wang J, Pan X, Liang X. Assessment for Melting Temperature Measurement of Nucleic Acid by HRM. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2016; 2016:5318935. [PMID: 27833775 PMCID: PMC5090098 DOI: 10.1155/2016/5318935] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/04/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
High resolution melting (HRM), with a high sensitivity to distinguish the nucleic acid species with small variations, has been widely applied in the mutation scanning, methylation analysis, and genotyping. For the aim of extending HRM for the evaluation of thermal stability of nucleic acid secondary structures on sequence dependence, we investigated effects of the dye of EvaGreen, metal ions, and impurities (such as dNTPs) on melting temperature (Tm ) measurement by HRM. The accuracy of HRM was assessed as compared with UV melting method, and little difference between the two methods was found when the DNA Tm was higher than 40°C. Both insufficiency and excessiveness of EvaGreen were found to give rise to a little bit higher Tm , showing that the proportion of dye should be considered for precise Tm measurement of nucleic acids. Finally, HRM method was also successfully used to measure Tm s of DNA triplex, hairpin, and RNA duplex. In conclusion, HRM can be applied in the evaluation of thermal stability of nucleic acid (DNA or RNA) or secondary structural elements (even when dNTPs are present).
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Affiliation(s)
- Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoming Pan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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38
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Jiang HX, Liang ZZ, Ma YH, Kong DM, Hong ZY. G-quadruplex fluorescent probe-mediated real-time rolling circle amplification strategy for highly sensitive microRNA detection. Anal Chim Acta 2016; 943:114-122. [PMID: 27769370 DOI: 10.1016/j.aca.2016.09.019] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 11/24/2022]
Abstract
Real-time PCR has revolutionized PCR from qualitative to quantitative. As an isothermal DNA amplification technique, rolling circular amplification (RCA) has been demonstrated to be a versatile tool in many fields. Development of a simple, highly sensitive, and specific strategy for real-time monitoring of RCA will increase its usefulness in many fields. The strategy reported here utilized the specific fluorescence response of thioflavin T (ThT) to G-quadruplexes formed by RCA products. Such a real-time monitoring strategy works well in both traditional RCA with linear amplification efficiency and modified RCA proceeded in an exponential manner, and can be readily performed in commercially available real-time PCR instruments, thereby achieving high-throughput detection and making the proposed technique more suitable for biosensing applications. As examples, real-time RCA-based sensing platforms were designed and successfully used for quantitation of microRNA over broad linear ranges (8 orders of magnitude) with a detection limit of 4 aM (or 0.12 zmol). The feasibility of microRNA analysis in human lung cancer cells was also demonstrated. This work provides a new method for real-time monitoring of RCA by using unique nucleic acid secondary structures and their specific fluorescent probes. It has the potential to be extended to other isothermal single-stranded DNA amplification techniques.
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Affiliation(s)
- Hong-Xin Jiang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin, 300071, PR China; Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, Nankai University, Tianjin, 300071, PR China
| | - Zhen-Zhen Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; College of Life Science, Nankai University, Tianjin, 300071, PR China
| | - Yan-Hong Ma
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; College of Life Science, Nankai University, Tianjin, 300071, PR China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin, 300071, PR China; Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Zhang-Yong Hong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; College of Life Science, Nankai University, Tianjin, 300071, PR China.
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39
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Ng S, Lim HS, Ma Q, Gao Z. Optical Aptasensors for Adenosine Triphosphate. Theranostics 2016; 6:1683-702. [PMID: 27446501 PMCID: PMC4955066 DOI: 10.7150/thno.15850] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/09/2016] [Indexed: 12/16/2022] Open
Abstract
Nucleic acids are among the most researched and applied biomolecules. Their diverse two- and three-dimensional structures in conjunction with their robust chemistry and ease of manipulation provide a rare opportunity for sensor applications. Moreover, their high biocompatibility has seen them being used in the construction of in vivo assays. Various nucleic acid-based devices have been extensively studied as either the principal element in discrete molecule-like sensors or as the main component in the fabrication of sensing devices. The use of aptamers in sensors - aptasensors, in particular, has led to improvements in sensitivity, selectivity, and multiplexing capacity for a wide verity of analytes like proteins, nucleic acids, as well as small biomolecules such as glucose and adenosine triphosphate (ATP). This article reviews the progress in the use of aptamers as the principal component in sensors for optical detection of ATP with an emphasis on sensing mechanism, performance, and applications with some discussion on challenges and perspectives.
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Affiliation(s)
| | | | | | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, Singapore 117543
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40
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Hollenstein M. Generation of long, fully modified, and serum-resistant oligonucleotides by rolling circle amplification. Org Biomol Chem 2016; 13:9820-4. [PMID: 26273951 DOI: 10.1039/c5ob01540e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rolling Circle Amplification (RCA) is an isothermal enzymatic method generating single-stranded DNA products consisting of concatemers containing multiple copies of the reverse complement of the circular template precursor. Little is known on the compatibility of modified nucleoside triphosphates (dN*TPs) with RCA, which would enable the synthesis of long, fully modified ssDNA sequences. Here, dNTPs modified at any position of the scaffold were shown to be compatible with rolling circle amplification, yielding long (>1 kb), and fully modified single-stranded DNA products. This methodology was applied for the generation of long, cytosine-rich synthetic mimics of telomeric DNA. The resulting modified oligonucleotides displayed an improved resistance to fetal bovine serum.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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41
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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42
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Huang BH, Geng ZR, Ma XY, Zhang C, Zhang ZY, Wang ZL. Lysosomal ATP imaging in living cells by a water-soluble cationic polythiophene derivative. Biosens Bioelectron 2016; 83:213-20. [PMID: 27131993 DOI: 10.1016/j.bios.2016.04.064] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 12/27/2022]
Abstract
Lysosomes in astrocytes and microglia can release ATP as the signaling molecule for the cells through ca(2+)-dependent exocytosis in response to various stimuli. At present, fluorescent probes that can detect ATP in lysosomes have not been reported. In this work, we have developed a new water-soluble cationic polythiophene derivative that can be specifically localized in lysosomes and can be utilized as a fluorescent probe to sense ATP in cells. PEMTEI exhibits high selectivity and sensitivity to ATP at physiological pH values and the detection limit of ATP is as low as 10(-11)M. The probe has low cytotoxicity, good permeability and high photostability in living cells and has been applied successfully to real-time monitoring of the change in concentrations of ATP in lysosomes though fluorescence microscopy. We also demonstrated that lysosomes in Hela cells can release ATP through Ca(2+)-dependent exocytosis in response to drug stimuli.
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Affiliation(s)
- Bing-Huan Huang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Zhi-Rong Geng
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China.
| | - Xiao-Yan Ma
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Cui Zhang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Zhi-Yang Zhang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Zhi-Lin Wang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China.
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Li X, Zheng F, Ren R. Detecting miRNA by producing RNA: a sensitive assay that combines rolling-circle DNA polymerization and rolling circle transcription. Chem Commun (Camb) 2016; 51:11976-9. [PMID: 26120604 DOI: 10.1039/c5cc01748c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Target miRNA was detected by producing RNA: rolling circle polymerization (RCP) and rolling circle transcription (RCT) were interlinked to provide dual amplification, producing multiplied malachite green (MG) aptamers, and a signal was generated by the SERS (surface-enhanced Raman scattering) quantification of the MG molecules that were bound to the transcripts.
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Affiliation(s)
- Xuemei Li
- Shandong Province 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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Zhao T, Lin C, Yao Q, Chen X. A label-free electrochemiluminescent sensor for ATP detection based on ATP-dependent ligation. Talanta 2016; 154:492-7. [PMID: 27154705 DOI: 10.1016/j.talanta.2016.03.091] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/21/2016] [Accepted: 03/28/2016] [Indexed: 11/26/2022]
Abstract
In this work, we describe a new label-free, sensitive and highly selective strategy for the electrochemiluminescent (ECL) detection of ATP at the picomolar level via ATP-induced ligation. The molecular-beacon like DNA probes (P12 complex) are self-assembled on a gold electrode. The presence of ATP leads to the ligation of P12 complex which blocks the digestion by Exonuclease III (Exo III). The protected P12 complex causes the intercalation of numerous ECL indicators (Ru(phen)3(2+)) into the duplex DNA grooves, resulting in significantly amplified ECL signal output. Since the ligating site of T4 DNA ligase and the nicking site of Exo III are the same, it involves no long time of incubation for conformation change. The proposed strategy combines the amplification power of enzyme and the inherent high sensitivity of the ECL technique and enables picomolar detection of ATP. The developed strategy also shows high selectivity against ATP analogs, which makes our new label-free and highly sensitive ligation-based method a useful addition to the amplified ATP detection arena.
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Affiliation(s)
| | - Chunshui Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Qiuhong Yao
- Xiamen Huaxia University, Xiamen 361024, China
| | - Xi Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China.
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Zhu Y, Wang H, Wang L, Zhu J, Jiang W. Cascade Signal Amplification Based on Copper Nanoparticle-Reported Rolling Circle Amplification for Ultrasensitive Electrochemical Detection of the Prostate Cancer Biomarker. ACS APPLIED MATERIALS & INTERFACES 2016; 8:2573-2581. [PMID: 26765624 DOI: 10.1021/acsami.5b10285] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An ultrasensitive and highly selective electrochemical assay was first attempted by combining the rolling circle amplification (RCA) reaction with poly(thymine)-templated copper nanoparticles (CuNPs) for cascade signal amplification. As proof of concept, prostate specific antigen (PSA) was selected as a model target. Using a gold nanoparticle (AuNP) as a carrier, we synthesized the primer-AuNP-aptamer bioconjugate for signal amplification by increasing the primer/aptamer ratio. The specific construction of primer-AuNP-aptamer/PSA/anti-PSA sandwich structure triggered the effective RCA reaction, in which thousands of tandem poly(thymine) repeats were generated and directly served as the specific templates for the subsequent CuNP formation. The signal readout was easily achieved by dissolving the RCA product-templated CuNPs and detecting the released copper ions with differential pulse stripping voltammetry. Because of the designed cascade signal amplification strategy, the newly developed method achieved a linear range of 0.05-500 fg/mL, with a remarkable detection limit of 0.020 ± 0.001 fg/mL PSA. Finally, the feasibility of the developed method for practical application was investigated by analyzing PSA in the real clinical human serum samples. The ultrasensitivity, specificity, convenience, and capability for analyzing the clinical samples demonstrate that this method has great potential for practical disease diagnosis applications.
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Affiliation(s)
- Ye Zhu
- Key Laboratory of Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University , Jinan 250100, China
| | - Huijuan Wang
- School of Pharmaceutical Sciences, Shandong University , Jinan 250012, China
| | - Lin Wang
- Department of Radiation Oncology, Qilu Hospital, Shandong University , Jinan 250012, China
| | - Jing Zhu
- Key Laboratory of Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University , Jinan 250100, China
| | - Wei Jiang
- Key Laboratory of Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University , Jinan 250100, China
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47
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Seok Kim Y, Ahmad Raston NH, Bock Gu M. Aptamer-based nanobiosensors. Biosens Bioelectron 2016; 76:2-19. [DOI: 10.1016/j.bios.2015.06.040] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/10/2015] [Accepted: 06/17/2015] [Indexed: 01/24/2023]
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48
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Li K, Wang L, Xu X, Gao T, Yan P, Jiang W. Protein binding-protected DNA three-way junction-mediated rolling circle amplification for sensitive and specific detection of transcription factors. RSC Adv 2016. [DOI: 10.1039/c6ra12535b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A novel fluorescent strategy for transcription factors assay was developed based on protein binding-protected DNA three-way junction-mediated rolling circle amplification.
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Affiliation(s)
- Kan Li
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Lei Wang
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
- P. R. China
| | - Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Ting Gao
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Ping Yan
- Jinan Maternity and Child Care Hospital
- 250001 Jinan
- P. R. China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
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Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges. Anal Bioanal Chem 2015; 408:2793-811. [DOI: 10.1007/s00216-015-9240-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/13/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022]
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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