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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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2
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Iwe IA, Li Z, Huang J. A dual-cycling fluorescence scheme for ultrasensitive DNA detection through signal amplification and target regeneration. Analyst 2019; 144:2649-2655. [PMID: 30843550 DOI: 10.1039/c9an00075e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, we propose an ultrasensitive fluorescence strategy for DNA detection. This method utilizes a molecular beacon (MB), a hairpin probe (HP), and an enzyme to trigger dual-cycling reactions (cycles I and II). In cycle I, the target is repeatedly used to amplify the fluorescence emission through hybridizations with the MB and cleavage reactions achieved by the enzyme. In cycle II, hybridization reactions between the HP and a segment of the MB continuously regenerate the target to trigger more cycle I reactions, leading to an enhanced fluorescent signal. The detection limit of the method is determined to be as low as 50 fM within 45 min, which is 2 to 3 orders of magnitude lower than that of the conventional fluorescence strategies. The method also shows a high selectivity over mismatched and random DNA sequences. The signal amplification mechanism of the strategy offers insights into constructing efficient and ultrasensitive biosensors for various applications.
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Affiliation(s)
- Idorenyin A Iwe
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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3
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Wang Y, Zhang L, Shen L, Ge S, Yu J, Yan M. Electrochemiluminescence DNA biosensor based on the use of gold nanoparticle modified graphite-like carbon nitride. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2234-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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4
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Gui Z, Wang Q, Li J, Zhu M, Yu L, Xun T, Yan F, Ju H. Direct detection of circulating free DNA extracted from serum samples of breast cancer using locked nucleic acid molecular beacon. Talanta 2016; 154:520-5. [PMID: 27154709 DOI: 10.1016/j.talanta.2016.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/25/2016] [Accepted: 04/03/2016] [Indexed: 12/24/2022]
Abstract
As an emerging noninvasive blood biomarker, circulating free DNA (cfDNA) can be utilized to assess diagnosis, progression and evaluate prognosis of cancer. However, cfDNAs are not "naked", they can be part of complexes, or are bound to the surface of the cells via proteins, which make the detection more challenging. Here, a simple method for the detection of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) DNA exacted from serum of breast cancer (BC) has been developed using a novel locked nucleic acid molecular beacon (LNA-MB). In order to enhance the stability and detection efficiency of the probe in biofluids, we design a shared-stem molecular beacon containing a 27-mer loop and a 4-mer stem with DNA/LNA alternating bases. The fluorescence is released in the presence of target. The detection procedure is simple and can be completed within 1h. This method shows a sensitive response to UHRF1 DNA with a dynamic range of 3 orders of magnitude. The limit of detection is 11nM (S/N=3) with excellent selectivity. It can discriminate UHRF1 DNA from three-base mismatched DNA with a high specificity. More importantly, this method can distinguish the expression of serum UHRF1 DNA among 5 breast cancer patients and 5 healthy controls. The mentioned superiority may suggest that this assay can be served as a promising noninvasive detection tool for early BC diagnosis and monitoring.
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Affiliation(s)
- Zhen Gui
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Cancer Hospital & Jiangsu Cancer Hospital, Nanjing 210009, PR China
| | - Quanbo Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, PR China
| | - Jinchang Li
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Cancer Hospital & Jiangsu Cancer Hospital, Nanjing 210009, PR China
| | - Mingchen Zhu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Cancer Hospital & Jiangsu Cancer Hospital, Nanjing 210009, PR China
| | - Lili Yu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Cancer Hospital & Jiangsu Cancer Hospital, Nanjing 210009, PR China
| | - Tang Xun
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Cancer Hospital & Jiangsu Cancer Hospital, Nanjing 210009, PR China
| | - Feng Yan
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Cancer Hospital & Jiangsu Cancer Hospital, Nanjing 210009, PR China.
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, PR China.
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5
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Ngavouka MDN, Capaldo P, Ambrosetti E, Scoles G, Casalis L, Parisse P. Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:220-227. [PMID: 26977379 PMCID: PMC4778512 DOI: 10.3762/bjnano.7.20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/25/2016] [Indexed: 01/10/2023]
Abstract
Background: DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA base-pairing that guarantee a high grade of selectivity. Nonetheless the presence of single base mismatches or not perfectly matched sequences can affect the response of the devices and the major challenge is, nowadays, to distinguish a mismatch of a single base and, at the same time, unequivocally differentiate devices read-out of fully and partially matching sequences. Results: We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic force microscopy-based nanolithography to create ssDNA nano-arrays on gold surfaces. AFM topography measurements then monitor the variation of height of the nanostructures upon biorecognition and then follow annealing at different temperatures. This strategy allowed us to clearly detect the presence of mismatches. The second strategy exploits the change in capacitance at the interface between an ssDNA-functionalized gold electrode and the solution due to the hybridization process in a miniaturized electrochemical cell. Through electrochemical impedance spectroscopy measurements on extended ssDNA self-assembled monolayers we followed in real-time the variation of capacitance, being able to distinguish, through the difference in hybridization kinetics, not only the presence of single, double or triple mismatches in the complementary sequence, but also the position of the mismatched base pair with respect to the electrode surface. Conclusion: We demonstrate here two platforms based on different sensing strategies as sensitive and selective tools to discriminate mismatches. Our assays are ready for parallelization and can be used in the detection and quantification of single nucleotide mismatches in microRNAs or in genomic DNA.
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Affiliation(s)
- Maryse D Nkoua Ngavouka
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Pietro Capaldo
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Elena Ambrosetti
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Giacinto Scoles
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy
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6
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Wegman DW, Ghasemi F, Stasheuski AS, Khorshidi A, Yang BB, Liu SK, Yousef GM, Krylov SN. Achieving Single-Nucleotide Specificity in Direct Quantitative Analysis of Multiple MicroRNAs (DQAMmiR). Anal Chem 2016; 88:2472-7. [PMID: 26756139 DOI: 10.1021/acs.analchem.5b04682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Direct quantitative analysis of multiple miRNAs (DQAMmiR) utilizes CE with fluorescence detection for fast, accurate, and sensitive quantitation of multiple miRNAs. Here we report on achieving single-nucleotide specificity and, thus, overcoming a principle obstacle on the way of DQAMmiR becoming a practical miRNA analysis tool. In general, sequence specificity is reached by raising the temperature to the level at which the probe-miRNA hybrids with mismatches melt while the matches remain intact. This elevated temperature is used as the hybridization temperature. Practical implementation of this apparently trivial approach in DQAMmiR has two major challenges. First, melting temperatures of all mismatched hybrids should be similar to each other and should not reach the melting temperature of any of the matched hybrids. Second, the elevated hybridization temperature should not deteriorate CE separation of the hybrids from the excess probes and the hybrids from each other. The second problem is further complicated by the reliance of separation in DQAMmiR on single-strand DNA binding protein (SSB) whose native structure and binding properties may be drastically affected by the elevated temperature. These problems were solved by two approaches. First, locked nucleic acid (LNA) bases were incorporated into the probes to normalize the melting temperatures of all target miRNA hybrids allowing for a single hybridization temperature; binding of SSB was not affected by LNA bases. Second, a dual-temperature CE was developed in which separation started with a high capillary temperature required for proper hybridization and continued at a low capillary temperature required for quality electrophoretic separation of the hybrids from excess probes and the hybrids from each other. The developed approach was sufficiently robust to allow its integration with sample preconcentration by isotachophoresis to achieve a limit of detection below 10 pM.
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Affiliation(s)
- David W Wegman
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Farhad Ghasemi
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Alexander S Stasheuski
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Anna Khorshidi
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Burton B Yang
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Stanley K Liu
- Sunnybrook-Odette Cancer Centre , 2075 Bayview Avenue, Toronto, Ontario M4N 3M5, Canada
| | - George M Yousef
- Keenan Research Centre, St. Michael's Hospital , 30 Bond Street, Toronto, Ontario M5B 1W8, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
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Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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8
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Huang J, Wang Z, Kim JK, Su X, Li Z. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide. Anal Chem 2015; 87:12254-61. [DOI: 10.1021/acs.analchem.5b03369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiahao Huang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhenyu Wang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jang-Kyo Kim
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public
Health and Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong
| | - Zhigang Li
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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9
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He Y, Huang G, Cui H. Quenching the chemiluminescence of acridinium ester by graphene oxide for label-free and homogeneous DNA detection. ACS APPLIED MATERIALS & INTERFACES 2013; 5:11336-11340. [PMID: 24090035 DOI: 10.1021/am404138x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
It was found that graphene oxide (GO) could effectively quench the chemiluminescence (CL) emission from a acridinium ester (AE)-hydrogen peroxide system. By taking advantage of this quenching effect, as a proof of concept, a label-free and homogeneous DNA assay was developed for the detection of Mycobacterium tuberculosis DNA. In the absence of target DNA, both probe DNA and AE were absorbed on the surface of GO, producing a weak CL emission owing to the CL quenching effect of GO. However, in the presence of target DNA, a double-stranded structure of DNA was generated, leading to the release of the oligonucleotide from the GO surface. AE favors binding with double-stranded DNA, which will be released from the GO surface; thus, the quenching effect of GO will be no longer effective and a strong CL signal can be observed. This assay can detect M. tuberculosis DNA with a detection limit of 0.65 nM. This sensitivity is lower than that of previously reported electrochemical detection.
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Affiliation(s)
- Yi He
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China , Hefei, Anhui 230026, P. R. China
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10
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Wang Q, Chen L, Long Y, Tian H, Wu J. Molecular beacons of xeno-nucleic acid for detecting nucleic acid. Theranostics 2013; 3:395-408. [PMID: 23781286 PMCID: PMC3677410 DOI: 10.7150/thno.5935] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/10/2013] [Indexed: 12/24/2022] Open
Abstract
Molecular beacons (MBs) of DNA and RNA have aroused increasing interest because they allow a continuous readout, excellent spatial and temporal resolution to observe in real time. This kind of dual-labeled oligonucleotide probes can differentiate between bound and unbound DNA/RNA in homogenous hybridization with a high signal-to-background ratio in living cells. This review briefly summarizes the different unnatural sugar backbones of oligonucleotides combined with fluorophores that have been employed to sense DNA/RNA. With different probes, we epitomize the fundamental understanding of driving forces and these recognition processes. Moreover, we will introduce a few novel and attractive emerging applications and discuss their advantages and disadvantages. We also highlight several perspective probes in the application of cancer therapeutics.
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11
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Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Anal Bioanal Chem 2012; 402:3071-89. [PMID: 22297860 DOI: 10.1007/s00216-012-5742-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/12/2012] [Indexed: 01/06/2023]
Abstract
Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.
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12
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Yin H, Zhou Y, Chen C, Zhu L, Ai S. An electrochemical signal ‘off–on’ sensing platform for microRNA detection. Analyst 2012; 137:1389-95. [DOI: 10.1039/c2an16098f] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Nakano K, Yamanouchi H, Yoshinaga H, Soh N, Imato T. Label-free DNA detection platform based on atomic force microscopy visualisation: characterising the molecular-recognition-triggered conformational changes of an immobilised receptor oligonucleotide probe. Chem Commun (Camb) 2010; 46:5683-5. [PMID: 20596585 DOI: 10.1039/c002642e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using atomic microscopy imaging, probe DNA sequence self-assemblies developed on Si(100) substrates undergo a conformational transition from an extended stem-loop structure to a double helix; such assemblies readily report on DNA molecular recognition events and should be suitable as a label-free, DNA hybridisation assay platform.
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Affiliation(s)
- Koji Nakano
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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