1
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Lee H, You J, Lee H, Kim W, Jang K, Park J, Na S. Enhanced selective discrimination of point-mutated viral RNA through false amplification regulatory direct insertion in rolling circle amplification. Biosens Bioelectron 2024; 252:116145. [PMID: 38412685 DOI: 10.1016/j.bios.2024.116145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
Coronaviruses are single-stranded RNA viruses with high mutation rates. Although a diagnostic method for coronaviruses has been developed, variants appear rapidly. Low test accuracy owing to single-point mutations is one of the main factors in the failure to prevent the early spread of coronavirus infection. Although reverse transcription-quantitative polymerase chain reaction can detect coronavirus infection, it cannot exclude the possibility of false positives, and an additional multiplexing kit is needed to discriminate single nucleotide polymorphism (SNP) variants. Therefore, in this study, we introduced a new nucleic acid amplification method to determine whether an infected person has a SNP mutation using a lateral flow assay (LFA) as a point-of-care test. Unlike traditional DNA amplification methods, direct insertion into rolling circle amplification amplifies the target genes without false amplification. After SNP-selective nucleic acid amplification, nuclease enzymes are used to make double-stranded DNA fragments that the LFA can detect, where specific mismatched DNA is found and cleaved to show different signals when a SNP-type is present. Therefore, wild- and SNP-type variants can be selectively detected. In this study, the limit of detection was 400 aM for viral RNA, and we successfully identified a dominant SNP variant selectively. Clinical tests were also conducted.
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Affiliation(s)
- Hakbeom Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Juneseok You
- Department of Mechanical Engineering, Kumoh National Institute of Technology, Gumi, 31977, Republic of Korea
| | - Hansol Lee
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woojoo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kuewhan Jang
- School of Mechanical Engineering, Hoseo University, Asan, 31499, Republic of Korea.
| | - Jinsung Park
- Department of Biomechatronics Engineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Suwon, 16419, Republic of Korea.
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea.
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2
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Chang D, Li J, Liu R, Liu M, Tram K, Schmitt N, Li Y. A Colorimetric Biosensing Platform with Aptamers, Rolling Circle Amplification and Urease-Mediated Litmus Test. Angew Chem Int Ed Engl 2023; 62:e202315185. [PMID: 37903738 DOI: 10.1002/anie.202315185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Here we report on an ultra-sensitive colorimetric sensing platform that takes advantage of both the strong amplification power of rolling circle amplification (RCA) and the high efficiency of a simple urease-mediated litmus test. The presence of a target triggers the RCA reaction, and urease-labelled DNA can hybridize to the biotinylated RCA products and be immobilized onto streptavidin-coated magnetic beads. The urease-laden beads are then used to hydrolyze urea, leading to an increase in pH that can be detected by a simple litmus test. We show this sensing platform can be easily integrated with aptamers for sensing diverse targets via the detection of human thrombin and platelet-derived growth factor (PDGF) utilizing structure-switching aptamers as well as SARS-CoV-2 in human saliva using a spike-binding trimeric DNA aptamer. Furthermore, we demonstrate that this colorimetric sensing platform can be integrated into a simple paper-based device for sensing applications.
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Affiliation(s)
- Dingran Chang
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Jiuxing Li
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Rudi Liu
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Meng Liu
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Kha Tram
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Natalie Schmitt
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Yingfu Li
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
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3
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Niu C, Liu J, Xing X, Zhang C. Exploring the Trans-Cleavage Activity with Rolling Circle Amplification for Fast Detection of miRNA. BIODESIGN RESEARCH 2023; 5:0010. [PMID: 37849464 PMCID: PMC10085249 DOI: 10.34133/bdr.0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/28/2023] [Indexed: 10/19/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous short noncoding RNA. They regulate gene expression and function, essential to biological processes. It is necessary to develop an efficient detection method to determine these valuable biomarkers for the diagnosis of cancers. In this paper, we proposed a general and rapid method for sensitive and quantitative detection of miRNA by combining CRISPR-Cas12a and rolling circle amplification (RCA) with the precircularized probe. Eventually, the detection of miRNA-21 could be completed in 70 min with a limit of detection of 8.1 pM with high specificity. The reaction time was reduced by almost 4 h from more than 5 h to 70 min, which makes detection more efficient. This design improves the efficiency of CRISPR-Cas and RCA-based sensing strategy and shows great potential in lab-based detection and point-of-care test.
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Affiliation(s)
- Chenqi Niu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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4
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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5
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Zeng H, Zhou H, Lin J, Pang Q, Chen S, Lin S, Xue C, Shen Z. Palindrome-Embedded Hairpin Structure and Its Target-Catalyzed Padlock Cyclization for Label-Free MicroRNA-Initiated Rolling Circle Amplification. ACS OMEGA 2023; 8:2253-2261. [PMID: 36687024 PMCID: PMC9850459 DOI: 10.1021/acsomega.2c06532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Highly sensitive detection of microRNAs (miRNAs) is of great significance in early diagnosis of cancers. Here, we develop a palindrome-embedded hairpin structure and its target-catalyzed padlock cyclization for rolling circle amplification, named PHP-RCA for simplicity, which can be applied in label-free ultrasensitive detection of miRNA. PHP-RCA is a facile system that consists of only an oligonucleotide probe with a palindrome-embedded hairpin structure (PHP). The two ends of PHP were extended as overhangs and designed with the complementary sequences of the target. Hence, the phosphorylated PHP can be cyclized by T4 DNA ligase in the presence of the target that serves as the ligation template. This ligation has formed a palindrome-embedded dumbbell-shaped probe (PDP) that allows phi29 polymerase to perform a typical target-primed RCA on PDP by taking miRNA as a primer, resulting in the production of a lengthy tandem repeat. Benefits from the palindromic sequences and hairpin-shaped structure in padlock double-stranded structures can be infinitely produced during the RCA reaction and provide numerous binding sites for SYBR Green I, a double-stranded dye, achieving a sharp response signal for label-free target detection. We have demonstrated that the proposed system exhibits a good linear range from 0.1 fM to 5 nM with a low detection limit of 0.1 fM, and the non-target miRNA can be clearly distinguished. The advantages of high efficiency, label-free signaling, and the use of only one oligonucleotide component make the PHP-RCA suitable for ultrasensitive, economic, and convenient detection of target miRNAs. This simple and powerful system is expected to provide a promising platform for tumor diagnosis, prognosis, and therapy.
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Affiliation(s)
- Huaiwen Zeng
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Hongyin Zhou
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
| | - Junliang Lin
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Qi Pang
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Siqiang Chen
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Shaoqi Lin
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Chang Xue
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
| | - Zhifa Shen
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
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6
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Target-Responsive Template Structure Switching-Mediated Exponential Rolling Circle Amplification for the Direct and Sensitive Detection of MicroRNA. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00071-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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7
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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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8
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Ahn SY, Liu J, Vellampatti S, Wu Y, Um SH. DNA Transformations for Diagnosis and Therapy. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2008279. [PMID: 33613148 PMCID: PMC7883235 DOI: 10.1002/adfm.202008279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Indexed: 05/03/2023]
Abstract
Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.
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Affiliation(s)
- So Yeon Ahn
- School of Chemical EngineeringSungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
| | - Jin Liu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Srivithya Vellampatti
- Institute of Convergent Chemical Engineering and TechnologySungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Present address:
Progeneer, Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Soong Ho Um
- School of Chemical EngineeringSKKU Advanced Institute of Nanotechnology (SAINT)Biomedical Institute for Convergence at SKKU (BICS) and Institute of Quantum Biophysics (IQB)Sungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Progeneer Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
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9
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Long N, Qiao Y, Xu Z, Tu J, Lu Z. Recent advances and application in whole-genome multiple displacement amplification. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0217-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Affiliation(s)
- Mohamed Sharafeldin
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Jason J. Davis
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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11
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Kim J, Ahn JK, Kim JS, Choi BR, Cho J, Lee H. Highly selective detection of single nucleotide polymorphism (SNP) using a dumbbell DNA probe with a gap-filling approach. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.03.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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Li XY, Cui YX, Du YC, Tang AN, Kong DM. Isothermal cross-boosting extension–nicking reaction mediated exponential signal amplification for ultrasensitive detection of polynucleotide kinase. Analyst 2020; 145:3742-3748. [DOI: 10.1039/c9an02569c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel nucleic acid-based isothermal signal amplification strategy, named cross-boosting extension–nicking reaction (CBENR) is developed and successfully used for rapid and ultrasensitive detection of polynucleotide kinase (PNK) activity.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
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13
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Sun H, Kong J, Wang Q, Liu Q, Zhang X. Dual Signal Amplification by eATRP and DNA-Templated Silver Nanoparticles for Ultrasensitive Electrochemical Detection of Nucleic Acids. ACS APPLIED MATERIALS & INTERFACES 2019; 11:27568-27573. [PMID: 31313584 DOI: 10.1021/acsami.9b08037] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Herein, an ultrasensitive and novel platform for DNA detection is reported, which combines DNA-templated silver nanoparticles (AgNPs) with electrochemical atom transfer radical polymerization signal amplification. Peptide nucleic acid (PNA) functionalized with thiol was modified to the Au electrode surface as a probe to specifically capture target DNA (T-DNA). After Zr4+ binds to phosphate on DNA, the initiator [α-bromophenylacetic acid (BPAA)] of ATRP is attached to PNA/DNA heteroduplexes based on the phosphate groups of T-DNA and carboxylate groups of BPAA via zirconium-phosphate-carboxylate chemistries. A large number of glyco-syloxyethyl methacrylates (GEMA) were captured on the formed PNA/DNA duplex via ATRP. Afterwards, the polysaccharides were oxidized to polymerized aldehydes with sodium periodate (NaIO4). In addition, AgNPs were deposited on the electrode surface by silver mirror reaction. The results indicate that the amount of AgNPs proportional to the T-DNA was quantified through differential pulse voltammetry. Furthermore, it proves that the modified electrode has good performance in DNA detection, indicating that the DNA sensor has high selectivity, high sensitivity, and stable repeatability. Under the optimal conditions, a good linear relationship is obtained in the range of 10 aM to 10 pM with the correlation coefficient of 0.992, and the detection limit is calculated to be as low as 4.725 aM. In addition, the sensor is successfully used to detect DNA in actual serum samples with satisfactory results, which indicates huge promise for detecting gene biomarkers and clinical analysis.
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Affiliation(s)
- Haobo Sun
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , P. R. China
| | - Jinming Kong
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , P. R. China
| | - Qiangwei Wang
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , P. R. China
| | - Qianrui Liu
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , P. R. China
| | - Xueji Zhang
- School of Biomedical Engineering , Shenzhen University Health Science Center , Shenzhen , Guangdong 518060 , P. R. China
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14
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Li X, Cui Y, Du Y, Tang A, Kong D. Label-Free Telomerase Detection in Single Cell Using a Five-Base Telomerase Product-Triggered Exponential Rolling Circle Amplification Strategy. ACS Sens 2019; 4:1090-1096. [PMID: 30945529 DOI: 10.1021/acssensors.9b00334] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Telomerase is a universal biomarker of malignant tumors. Sensitive and reliable analysis for telomerase activity is of vital importance for both early diagnosis and therapy of malignant tumors. Herein, a novel fluorescent strategy was proposed for sensitive and label-free detection of telomerase activity. One highlight of this strategy is that an exponential signal amplification can be triggered by a very short telomerase extension product (TEP). Without adding dATP, the designed telomerase primer can be easily controlled to extend five bases (GGGTT) to give short TEP with definite length. The resulting short TEP can then be constructed as a circular rolling circle amplification (RCA) template and thus initiate a nicking enzyme-mediated exponential RCA, producing G-rich amplification products that can be sensitively probed via specific binding between the fluorescent dye Thioflavin T (ThT) and the nucleic acid G-quadruplexes. Elevated telomerase translocation efficiency, combined with exponential signal amplification and specific probing of RCA products by ThT, endow the sensing platform with extraordinarily high detection sensitivity. The requirement for short TEP increases the possibility to analyze telomerase with low activity. The proposed sensing platform can achieve sensitive telomerase activity detection in individual cells, even with the interference of accumulated normal cells. It was also demonstrated to show excellent capability in screening for the inhibitors of telomerase. Therefore, the proposed sensing platform has great potential for not only clinical diagnosis but also anticancer drug development.
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Affiliation(s)
- XiaoYu Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - YunXi Cui
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - YiChen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - AnNa Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - DeMing Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300071, P. R. China
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15
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Li S, Liu S, Xu Y, Zhang R, Zhao Y, Qu X, Wang Y, Huang J, Yu J. Robust and highly specific fluorescence sensing of Salmonella typhimurium based on dual-functional phi29 DNA polymerase-mediated isothermal circular strand displacement polymerization. Analyst 2019; 144:4795-4802. [DOI: 10.1039/c9an00843h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and robust fluorescence sensing strategy has been developed for the detection of pathogenic bacteria by the combination of the dual functionality of phi29 DNA polymerase with isothermal circular strand displacement polymerization (ICSDP).
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Affiliation(s)
- Shasha Li
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Su Liu
- School of Water Conservancy and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yicheng Xu
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Rufeng Zhang
- School of Water Conservancy and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yihan Zhao
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Xiaonan Qu
- School of Water Conservancy and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yu Wang
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Jiadong Huang
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- College of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
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16
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Yeasmin Khusbu F, Zhou X, Chen H, Ma C, Wang K. Thioflavin T as a fluorescence probe for biosensing applications. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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17
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Abrosimova LA, Migur AY, Kubareva EA, Zatsepin TS, Gavshina AV, Yunusova AK, Perevyazova TA, Pingoud A, Oretskaya TS. A study on endonuclease BspD6I and its stimulus-responsive switching by modified oligonucleotides. PLoS One 2018; 13:e0207302. [PMID: 30475809 PMCID: PMC6261011 DOI: 10.1371/journal.pone.0207302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/28/2018] [Indexed: 11/18/2022] Open
Abstract
Nicking endonucleases (NEases) selectively cleave single DNA strands in double-stranded DNAs at a specific site. They are widely used in bioanalytical applications and in genome editing; however, the peculiarities of DNA-protein interactions for most of them are still poorly studied. Previously, it has been shown that the large subunit of heterodimeric restriction endonuclease BspD6I (Nt.BstD6I) acts as a NEase. Here we present a study of interaction of restriction endonuclease BspD6I with modified DNA containing single non-nucleotide insertion with an azobenzene moiety in the enzyme cleavage sites or in positions of sugar-phosphate backbone nearby. According to these data, we designed a number of effective stimulus-responsive oligonucleotide inhibitors bearing azobenzene or triethylene glycol residues. These modified oligonucleotides modulated the functional activity of Nt.BspD6I after cooling or heating. We were able to block the cleavage of T7 phage DNA by this enzyme in the presence of such inhibitors at 20-25°C, whereas the Nt.BspD6I ability to hydrolyze DNA was completely restored after heating to 45°C. The observed effects can serve as a basis for the development of a platform for regulation of NEase activity in vitro or in vivo by external signals.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Anzhela Yu. Migur
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elena A. Kubareva
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Timofei S. Zatsepin
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia
| | - Aleksandra V. Gavshina
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alfiya K. Yunusova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Tatiana S. Oretskaya
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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18
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Qu X, Bian F, Guo Q, Ge Q, Sun Q, Huang X. Ligation-Rolling Circle Amplification on Quantum Dot-Encoded Microbeads for Detection of Multiplex G-Quadruplex-Forming Sequences. Anal Chem 2018; 90:12051-12058. [DOI: 10.1021/acs.analchem.8b02820] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiaojun Qu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Feika Bian
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingsheng Guo
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuebin Huang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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19
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Zingg JM, Daunert S. Trinucleotide Rolling Circle Amplification: A Novel Method for the Detection of RNA and DNA. Methods Protoc 2018. [PMCID: PMC6526412 DOI: 10.3390/mps1020015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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20
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Du YC, Zhu YJ, Li XY, Kong DM. Amplified detection of genome-containing biological targets using terminal deoxynucleotidyl transferase-assisted rolling circle amplification. Chem Commun (Camb) 2018; 54:682-685. [DOI: 10.1039/c7cc09337c] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We proposed a terminal deoxynucleotidyl transferase (TdT)-assisted rolling circle amplification (RCA) strategy for the amplified detection of genome-containing biological targets.
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Affiliation(s)
- Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Yan-Jun Zhu
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- College of Chemistry
- Nankai University
- Tianjin
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21
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Tenaglia E, Imaizumi Y, Miyahara Y, Guiducci C. Isothermal multiple displacement amplification of DNA templates in minimally buffered conditions using phi29 polymerase. Chem Commun (Camb) 2018; 54:2158-2161. [DOI: 10.1039/c7cc09609g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
phi29 can be used to amplify DNA and at constant temperature and minimally buffered conditions to produce pH readouts.
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Affiliation(s)
- Enrico Tenaglia
- Laboratory of Life Science Electronics (CLSE) – Institute of Bioengineering École Polythéchnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Yuki Imaizumi
- Institute of Biomaterials and Bioengineering
- Tokyo Medical and Dental University (TMDU)
- Tokyo 101-0062
- Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering
- Tokyo Medical and Dental University (TMDU)
- Tokyo 101-0062
- Japan
| | - Carlotta Guiducci
- Laboratory of Life Science Electronics (CLSE) – Institute of Bioengineering École Polythéchnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
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22
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Wu H, Zhou X, Cheng W, Yuan T, Zhao M, Duan X, Ding S. A simple fluorescence biosensing strategy for ultrasensitive detection of the BCR–ABL1 fusion gene based on a DNA machine and multiple primer-like rolling circle amplification. Analyst 2018; 143:4974-4980. [DOI: 10.1039/c8an01094c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A one-step, rapid fluorescence biosensing method has been developed for ultrasensitive detection of BCR–ABL1 fusion gene based on a DNA machine and multiple primer-like rolling circle amplification.
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Affiliation(s)
- Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)
- College of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- China
| | - Xiaoyan Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)
- College of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- China
| | - Wei Cheng
- The Center for Clinical Molecular Medical detection
- The First Affiliated Hospital of Chongqing Medical University
- Chongqing 400016
- China
| | - Taixian Yuan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)
- College of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)
- College of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- China
| | - Xiaolei Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)
- College of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)
- College of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- China
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