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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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Xu J, Jiang R, He H, Ma C, Tang Z. Recent advances on G-quadruplex for biosensing, bioimaging and cancer therapy. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116257] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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3
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Zhou X, Zhu Q, Yang Y. Aptamer-integrated nucleic acid circuits for biosensing: Classification, challenges and perspectives. Biosens Bioelectron 2020; 165:112422. [PMID: 32729540 DOI: 10.1016/j.bios.2020.112422] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 12/27/2022]
Abstract
Owing to their high programmability and modularity, autonomous enzyme-free nucleic acid circuits are attracting ever-growing interest as signal amplifiers with potential applications in developing highly sensitive biosensing techniques. Besides nucleic acid input, the biosensing scope of aptamer-integrated nucleic acids could be further expanded to non-nucleic targets by integrating nucleic acid circuits with aptamers-a class of functional oligonucleotides with binding capabilities toward specific targets. By coupling upstream target recognition with downstream signal amplification, aptamer-integrated nucleic acid circuits enable aptasensors with increased sensitivity and enhanced performances, which may act as powerful tools in various fields including environment monitoring, personal care, clinical diagnosis, etc. In designing aptamer-integrated nucleic acid circuits, smart integration between aptamer and nucleic acid circuits plays a crucial role in developing reliable circuits with good performances. To date, although there are plenty of published researches adopting aptamer-integrated nucleic acid circuits as amplifiers in biosensing systems, deep discussion or systematic review on rational design strategies for aptamer-integrated nucleic acid circuits is still lacking. To fill this gap, rational aptamer-nucleic acid circuits integration modes were classified and summarized for the first time based on reviewing the state of art of existing aptamer-integrated nucleic acid circuits. Moreover, theoretical updates in nucleic acid circuits designs and major challenges to be overcome in developing highly sensitive aptamer-integrated nucleic acids based biosensing systems are discussed in this review.
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Affiliation(s)
- Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Qian Zhu
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yihan Yang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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Qi W, Liu Z, Zhang W, Halawa MI, Xu G. Visual and Plasmon Resonance Absorption Sensor for Adenosine Triphosphate Based on the High Affinity between Phosphate and Zr(IV). SENSORS (BASEL, SWITZERLAND) 2016; 16:s16101674. [PMID: 27754349 PMCID: PMC5087462 DOI: 10.3390/s16101674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/19/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
Zr(IV) can form phosphate and Zr(IV) (-PO₃2--Zr4+-) complex owing to the high affinity between Zr(IV) with phosphate. Zr(IV) can induce the aggregation of gold nanoparticles (AuNPs), while adenosine triphosphate(ATP) can prevent Zr(IV)-induced aggregation of AuNPs. Herein, a visual and plasmon resonance absorption (PRA)sensor for ATP have been developed using AuNPs based on the high affinity between Zr(IV)with ATP. AuNPs get aggregated in the presence of certain concentrations of Zr(IV). After the addition of ATP, ATP reacts with Zr(IV) and prevents AuNPs from aggregation, enabling the detection of ATP. Because of the fast interaction of ATP with Zr(IV), ATP can be detected with a detection limit of 0.5 μM within 2 min by the naked eye. Moreover, ATP can be detected by the PRA technique with higher sensitivity. The A520nm/A650nm values in PRA spectra increase linearly with the concentrations of ATP from 0.1 μM to 15 μM (r = 0.9945) with a detection limit of 28 nM. The proposed visual and PRA sensor exhibit good selectivity against adenosine, adenosine monophosphate, guanosine triphosphate, cytidine triphosphate and uridine triphosphate. The recoveries for the analysis of ATP in synthetic samples range from 95.3% to 102.0%. Therefore, the proposed novel sensor for ATP is promising for real-time or on-site detection of ATP.
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Affiliation(s)
- Wenjing Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
- Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, China.
| | - Zhongyuan Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Wei Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Mohamed Ibrahim Halawa
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
- Chinese Academy of Sciences, University of Chinese Academy of Sciences, No. 19A Yuquanlu, Beijing 100049, China.
| | - Guobao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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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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Ma DL, Wang W, Mao Z, Kang TS, Han QB, Chan PWH, Leung CH. Utilization of G-Quadruplex-Forming Aptamers for the Construction of Luminescence Sensing Platforms. Chempluschem 2016; 82:8-17. [DOI: 10.1002/cplu.201600036] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/07/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Wanhe Wang
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Zhifeng Mao
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
| | - Quan-Bin Han
- School of Chinese Medicine; Hong Kong Baptist University; Kowloon Hong Kong 852 P. R. China
| | - Philip Wai Hong Chan
- School of Chemistry; Monash University; Clayton VIC 3800 Australia
- Department of Chemistry; University of Warwick; Coventry CV4 7AL United Kingdom
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
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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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Guo Y, Sun X, Yang G, Liu J. Ultrasensitive detection of ATP based on ATP regeneration amplification and its application in cell homogenate and human serum. Chem Commun (Camb) 2015; 50:7659-62. [PMID: 24898261 DOI: 10.1039/c4cc01458h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A conformation-switching aptamer molecule that could be circularized without ligation DNA was designed. Pyrophosphate (PPi) was converted to ATP, resulting in higher signals for ATP detection. Meanwhile, the method has significant implications for real applications.
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Affiliation(s)
- Yingshu Guo
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
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10
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Evaluating the dual target binding capabilities of immobilized aptamers using flow cytometry. Biointerphases 2015; 10:019015. [PMID: 25787142 DOI: 10.1116/1.4915107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the current study, the authors quantify the binding activity of particle-immobilized DNA aptamers to their nucleotide and non-nucleotide targets. For the purposes of this work, DNA and vascular endothelial growth factor (VEGF) binding analysis was carried out for VEGF-binding aptamers and compared to that of an ampicillin-binding aptamer as well as a non-aptamer DNA probe. Binding analysis followed incubation of one target type, coincubation of both DNA and VEGF targets, and serial incubations of each target type. Moreover, recovery of aptamer binding activity following displacement of the DNA target from aptamer:DNA duplexes was also explored. Flow cytometry served as the quantitative tool to directly monitor binding events of both the DNA target and protein target to the various aptamer and non-aptamer functionalized particles. The current work demonstrates how processing steps such as annealing and binding history of particle-immobilized aptamers can affect subsequent binding activity. To this end, the authors demonstrate the ability to fully recover DNA target binding activity capabilities and to partially recover protein target binding activity.
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Li F, Zhang H, Wang Z, Newbigging AM, Reid MS, Li XF, Le XC. Aptamers facilitating amplified detection of biomolecules. Anal Chem 2014; 87:274-92. [PMID: 25313902 DOI: 10.1021/ac5037236] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Feng Li
- Department of Laboratory Medicine and Pathology, ‡Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G3
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Oishi M, Nakao S, Kato D. Enzyme-free fluorescent-amplified aptasensors based on target-responsive DNA strand displacement via toehold-mediated click chemical ligation. Chem Commun (Camb) 2014; 50:991-3. [PMID: 24306006 DOI: 10.1039/c3cc48064j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new target-responsive DNA strand displacement system via toehold-mediated click chemical ligation was designed and prepared for enzyme-free fluorescent-amplified aptasensors. The aptasensors significantly amplified fluorescent signals in response to targets based on target recycling processes.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan.
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