1
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Yoon J, Lee J, Kim J, Lee SM, Kim S, Park HG. A novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension reaction. Biosens Bioelectron 2024; 253:116174. [PMID: 38432074 DOI: 10.1016/j.bios.2024.116174] [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: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
We herein present a novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction. The detection probe employed as a key component in this technique serves as a substrate for RNase H and triggers the PS-THSP reaction upon the RNase H-mediated degradation of the probe. As a consequence, a large number of long concatemeric amplification products could be produced and used to identify the RNase H activity through the fluorescence signals produced by the nucleic acid-specific fluorescent dye, SYTO 9. Importantly, the use of the gp32 protein allowed the PS-THSP reaction to be performed at 37 °C, ultimately enabling an isothermal one-step RNase H assay. Based on this sophisticated design principle, the RNase H activity was very sensitively detected, down to 0.000237 U mL-1 with high specificity. We further verified its practical applicability through its successful application to the screening of RNase H inhibitors. With its operational convenience and excellent analytical performance, this technique could serve as a new platform for RNase H assay in a wide range of biological applications.
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Affiliation(s)
- Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jinhwan Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jaemin Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Mo Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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2
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Wang H, Liu J, Fang Y, Shen X, Liu H, Yu L, Zeng S, Cai S, Zhou J, Li Z. Design and analysis of self-priming extension DNA hairpin probe for miRNA detection based on a unified dynamic programming framework. Anal Chim Acta 2024; 1303:342530. [PMID: 38609269 DOI: 10.1016/j.aca.2024.342530] [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: 12/19/2023] [Revised: 02/03/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
MicroRNAs (miRNAs) are potential biomarkers for cancer diagnosis and prognosis, methods for detecting miRNAs with high sensitivity, selectivity, and stability are urgently needed. Various nucleic acid probes that have traditionally been for this purpose suffer several drawbacks, including inefficient signal-to-noise ratios and intensities, high cost, and time-consuming method establishment. Computing tools used for investigating the thermodynamics of DNA hybridization reactions can accurately predict the secondary structure of DNA and the interactions between DNA molecules. Herein, NUPACK was used to design a series of nucleic acid probes and develop a phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) signal amplification strategy, which enabled the ultrasensitive detection of miR-200a in serum samples. The free and binding energies of the DNA detection probes calculated using NUPACK, as well as the biological experimental results, were considered synthetically to select the best sequence and experimental conditions. A unified dynamic programming framework, NUPACK analysis and the experimental data, were complementary and improved the designed model in all respects. Our study demonstrates the feasibility of using computer technology such as NUPACK to simplify the experimental process and provide intuitive results.
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Affiliation(s)
- Hecheng Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiatong Liu
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yanyan Fang
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xudan Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hui Liu
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310020, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Jingjing Zhou
- Beijing Lab for Cardiovascular Precision Medicine, Echocardiography Medical Center, Maternal-Fetal Medicine Center in Fetal Heart Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.
| | - Zheyong Li
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310020, China; Zhejiang University Sir Run Run Shaw Alaer Hospital, Alaer, Xinjiang, 843300, China.
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3
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Li D, Yao Y, Cheng W, Hou Z, Wang Z, Xiang Y. Self-Priming Cyclic Amplification Accelerating CRISPR Sensor for Sensitive and Specific MicroRNA Analysis with No Background. Anal Chem 2024; 96:1717-1724. [PMID: 38217876 DOI: 10.1021/acs.analchem.3c04866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
In this work, we demonstrate for the first time the application of the phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction for miRNA assays. A self-priming amplification accelerating CRISPR sensor was well-established for sensitive and specific miRNA detection by integrating the PS-THSP reaction and CRISPR/Cas12a system. The sensor consists of three steps: (1) the formation of a complete PS-THSP template in the presence of target miRNA and ligase; (2) the exponential isothermal amplification of the PS-THSP reaction under the action of DNA polymerase; (3) the activation of the CRISPR/Cas12a fluorescence system to generate signals. We used miR-21 as a model target. The sensor can achieve sensitive detection of miR-21 without the involvement of any primers, and the special design of the CRISPR proto-spacer neighbor motif (PAM) sequence effectively avoids the interference of the background signal. In addition, the sensor can not only identify single-base mutant homologous sequences but also show stable performance in complex biological matrices. We have successfully used this sensor to accurately analyze miR-21 in different cell lines and real clinical samples, demonstrating its great potential in clinical diagnosis.
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Affiliation(s)
- Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Yanheng Yao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Wenting Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Zhiqiang Hou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Zhongyun Wang
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, P. R. China
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4
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Yu L, Tang Z, Sun Y, Yi H, Tang Y, Zhong Y, Dian D, Cong Y, Wang H, Xie Z, He S, Chen Z. A polyethylene glycol enhanced ligation-triggered self-priming isothermal amplification for the detection of SARS-CoV-2 D614G mutation. Talanta 2023; 262:124711. [PMID: 37244245 DOI: 10.1016/j.talanta.2023.124711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
We presented a polyethylene glycol (PEG) enhanced ligation-triggered self-priming isothermal amplification (PEG-LSPA) for the detection D614G mutation in S-glycoprotein of SARS-CoV-2. PEG was employed to improve the ligation efficiency of this assay by constructing a molecular crowding environment. Two hairpin probes (H1 and H2) were designed to contain 18 nt and 20 nt target binding site at their 3' end and 5' end, respectively. In presence of target sequence, it complemented with H1 and H2 to trigger ligation by ligase under molecular crowding condition to form ligated H1-H2 duplex. Then 3' terminus of the H2 would be extended by DNA polymerase under isothermal conditions to form a longer extended hairpin (EHP1). 5' terminus of EHP1 with phosphorothioate (PS) modification could form hairpin structure due to the lower Tm value. The resulting 3' end overhang would also fold back as a new primer to initiate the next round of polymerization, resulting in the formation of a longer extended hairpin (EHP2) containing two target sequence domains. In the circle of LSPA, long extended hairpin (EHPx) containing numerous target sequence domains was produced. The resulting DNA products can be monitored in real-time fluorescence signaling. Our proposed assay owns an excellent linear range from 10 fM to 10 nM with a detection limit down to 4 fM. Thus, this work provides a potential isothermal amplification method for monitoring mutations in SARS-CoV-2 variants.
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Affiliation(s)
- Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zibin Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuanzhong Sun
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Hai Yi
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuebiao Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yangqing Zhong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Dongchun Dian
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Yanguang Cong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Houqi Wang
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zhaoyang Xie
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Suhui He
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Zhangquan Chen
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
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Wang Y, Zhang L, Shen Y, Yu EYW, Ding X. Nested Phosphorothioated Hybrid Primer-Mediated Isothermal Amplification for Specific and Dye-Based Subattomolar Nucleic Acid Detection at Low Temperatures. ACS Sens 2023; 8:1261-1271. [PMID: 36867102 DOI: 10.1021/acssensors.2c02754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Developing dye-based isothermal nucleic acid amplification (INAA) at low temperatures such as 37 °C remains a technical challenge. Here, we describe a nested phosphorothioated (PS) hybrid primer-mediated isothermal amplification (NPSA) assay which only utilizes EvaGreen (a DNA-binding dye) to achieve specific and dye-based subattomolar nucleic acid detection at 37 °C. The success of low-temperature NPSA essentially depends on employing Bacillus smithii DNA polymerase, a strand-displacing DNA polymerase with wide range of activation temperature. However, the NPSA's high efficiency entails nested PS-modified hybrid primers and the additives of urea and T4 Gene 32 Protein. To address the inhibition of urea on reverse transcription (RT), one-tube two-stage recombinase-aided RT-NPSA (rRT-NPSA) is established. By targeting human Kirsten rat sarcoma viral (KRAS) oncogene, NPSA (rRT-NPSA) stably detects 0.2 aM of KRAS gene (mRNA) within 90 (60) min. In addition, rRT-NPSA possesses subattomolar sensitivity to detect human ribosomal protein L13 mRNA. The NPSA/rRT-NPSA assays are also validated to obtain consistent results with PCR/RT-PCR methods on qualitatively detecting DNA/mRNA targets extracted from cultured cells and clinical samples. As a dye-based, low-temperature INAA method, NPSA inherently facilitates the development of miniaturized diagnostic biosensors.
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Affiliation(s)
- Yaru Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Lanxiang Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yuqing Shen
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Evan Yi-Wen Yu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Epidemiology & Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Xiong Ding
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
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6
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Moon J, Song J, Jang H, Kang H, Huh YM, Son HY, Rho HW, Park M, Talwar CS, Park KH, Woo E, Lim J, Lim EK, Jung J, Jung Y, Park HG, Kang T. Ligation-free isothermal nucleic acid amplification. Biosens Bioelectron 2022; 209:114256. [DOI: 10.1016/j.bios.2022.114256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 12/19/2022]
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7
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Jiang X, Shen X, Talap J, Yang D, Zeng S, Liu H, Cai S. Phosphorothioated and phosphate-terminal dumbbell (PP-TD) probe-based rapid detection of polynucleotide kinase activity. Analyst 2022; 147:4986-4990. [DOI: 10.1039/d2an01431a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A primer-free, sensitive assay has been developed to detect polynucleotide kinase (PNK) activity. This proposed method provides a promising platform for PNK activity monitoring and inhibition screening for drug discovery and clinical treatment.
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Affiliation(s)
- Xianfeng Jiang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, China
| | - Xudan Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Yang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
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8
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Glökler J, Lim TS, Ida J, Frohme M. Isothermal amplifications - a comprehensive review on current methods. Crit Rev Biochem Mol Biol 2021; 56:543-586. [PMID: 34263688 DOI: 10.1080/10409238.2021.1937927] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
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Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
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Jung Y, Song J, Park HG. Ultrasensitive nucleic acid detection based on phosphorothioated hairpin-assisted isothermal amplification. Sci Rep 2021; 11:8399. [PMID: 33863981 PMCID: PMC8052315 DOI: 10.1038/s41598-021-87948-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023] Open
Abstract
Herein, we describe a phosphorothioated hairpin-assisted isothermal amplification (PHAmp) method for detection of a target nucleic acid. The hairpin probe (HP) is designed to contain a 5' phosphorothioate (PS)-modified overhang, a target recognition site, and a 3' self-priming (SP) region. Upon binding to the target nucleic acid, the HP opens and the SP region is rearranged to serve as a primer. The subsequent process of strand displacement DNA synthesis recycles the bound target to open another HP and produces an extended HP (EP) with a PS-DNA/DNA duplex at the end, which would be readily denatured due to its reduced thermal stability. The trigger then binds to the denatured 3' end of the EP and is extended, producing an intermediate double-stranded (ds) DNA product (IP). The trigger also binds to the denatured 3' end of the IP, and its extension produces the final dsDNA product along with concomitant displacement and recycling of EP. By monitoring the dsDNA products, the target nucleic acid can be identified down to 0.29 fM with a wide dynamic range from 1 nM to 1 fM yielding an excellent specificity to discriminate even a single base-mismatched target. The unique design principle could provide new insights into the development of novel isothermal amplification methods for nucleic acid detection.
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Affiliation(s)
- Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Song J, Kim HY, Kim S, Jung Y, Park HG. Self-priming phosphorothioated hairpin-mediated isothermal amplification. Biosens Bioelectron 2021; 178:113051. [PMID: 33548651 DOI: 10.1016/j.bios.2021.113051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 01/06/2023]
Abstract
We herein describe a novel technology, termed self-priming phosphorothioated hairpin-mediated isothermal amplification (SP-HAMP), enabling target nucleic acid detection. Isothermal amplification strategies are a simple process that efficiently raises the amount of nucleic acid at a constant temperature, but still has lots of problems such as the requirement of multiple exogenous primers and enzymes, which trigger non-specific background signal and increase the complexity of procedures. The key component for overcoming the above-mentioned limitations is the designed hairpin probe (HP) consisting of self-priming region along the 3' stem and the 3' overhang and phosphorothioate modifications at the 5' overhang and the specific loop part. The HP was designed to open through binding to target nucleic acid. Upon opening of HP, its self-priming (SP) region is rearranged to form a smaller hairpin whose 3' end could serve as a primer. The following extension produces the extended HP and displaces the bound target nucleic acid, which is then recycled to open another HP. Due to the reduced stability caused by the specific two phosphorothioate (PS) modifications, the 3' end of EP1 is readily rearranged to form the foldback hairpin structure, which would promote the foldback extension to produce once more extended HP. Since the two PS modifications are always located at the same positions along the 5' stem within the further extended HPs, the foldback reaction followed by the extension would be continuously repeated, consequently producing a large number of the long hairpin concatamers. Based on this unique design principle, we successfully detected even a single copy of target DNA with outstanding discrimination capability under an isothermal condition by employing only a single HP without the requirement for the complicated multiple primers. In conclusion, the sophisticated design principle employed in this work would provide great insight for the development of self-operative isothermal amplifying system enabling short target nucleic acid detection such as microRNAs or any target which is less than 200 mer.
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Affiliation(s)
- Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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11
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Abdullah Al-Maskri AA, Ye J, Talap J, Hu H, Sun L, Yu L, Cai S, Zeng S. Reverse transcription-based loop-mediated isothermal amplification strategy for real-time miRNA detection with phosphorothioated probes. Anal Chim Acta 2020; 1126:1-6. [PMID: 32736712 DOI: 10.1016/j.aca.2020.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/22/2020] [Accepted: 06/02/2020] [Indexed: 12/27/2022]
Abstract
A novel reverse transcription-based loop-mediated isothermal amplification (LAMP) strategy for miRNA detection has been developed. This method consists of two stem-loop probes inspired by the dumbbell-shaped amplicons and inner primers used in conventional LAMP reactions. Termed "terminal hairpin formation and self-priming" (THSP), this reaction incorporates phosphorothioated (PS) modifications to achieve DNA folding and extension without primers. The final signal is monitored by a sequence-specific detection probe, which minimizes the background noise. We suggest that our rapid, facile, and reliable LAMP method will be a promising candidate for detecting miRNA in biomedical applications.
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Affiliation(s)
- Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haihong Hu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Park D, Ellington AD, Jung C. Selection of self-priming molecular replicators. Nucleic Acids Res 2019; 47:2169-2176. [PMID: 30698805 PMCID: PMC6412129 DOI: 10.1093/nar/gkz044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 11/29/2022] Open
Abstract
Self-priming amplification of oligonucleotides is possible based on foldback of 3′ ends, self-priming, and concatemerization, especially in the presence of phosphorothioate linkages. Such a simple replicative mechanism may have led to the accumulation of specific replicators at or near the origin of life. To determine how early replicators may have competed with one another, we have carried out selections with phosphorothiolated hairpins appended to a short random sequence library (N10). Upon the addition of deoxynucleoside triphosphates and a polymerase, concatemers quickly formed, and those random sequences that templated the insertion of purines, especially during initiation, quickly predominated. Over several serial transfers, particular sequences accumulated, and in isolation these were shown to outcompete less efficient replicators.
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Affiliation(s)
- Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Cheulhee Jung
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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Cai S, Jung C, Bhadra S, Ellington AD. Phosphorothioated Primers Lead to Loop-Mediated Isothermal Amplification at Low Temperatures. Anal Chem 2018; 90:8290-8294. [PMID: 29968462 DOI: 10.1021/acs.analchem.8b02062] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an extremely powerful tool for the detection of nucleic acids with high sensitivity and specificity. However, LAMP shows optimal performance at around 65 °C, which limits applications in point-of-care-testing (POCT). Here, we have developed a version of LAMP that uses phosphorothioated primers (PS-LAMP) to enable more efficient hairpin formation and extension at the termini of growing concatamers, and that therefore works at much lower temperatures. By including additional factors such as chaotropes (urea) and single-stranded DNA binding protein (SSB), the sensitivities and selectivities for amplicon detection with PS-LAMP at 40 °C were comparable with a regular LAMP reaction at 65 °C.
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Affiliation(s)
- Sheng Cai
- Laboratory of Pharmaceutical Analysis and Drug Metabolism, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Cheulhee Jung
- Division of Biotechnology , College of Life Sciences and Biotechnology, Korea University , Seoul 02841 , Republic of Korea
| | - Sanchita Bhadra
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas at Austin , Austin , Texas 78712 , United States
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Schaffter SW, Green LN, Schneider J, Subramanian HKK, Schulman R, Franco E. T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures. Nucleic Acids Res 2018; 46:5332-5343. [PMID: 29718412 PMCID: PMC6007251 DOI: 10.1093/nar/gky283] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/18/2022] Open
Abstract
The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
| | - Leopold N Green
- Department of Mechanical Engineering – University of California - Riverside
| | - Joanna Schneider
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
| | | | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
- Department of Computer Science – Johns Hopkins University
| | - Elisa Franco
- Department of Mechanical Engineering – University of California - Riverside
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