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Mao J, Tang S, Liang S, Pan W, Kang Y, Cheng J, Yu D, Chen J, Lou J, Zhao H, Zhou J. A new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of exponential amplification reaction. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3947-3953. [PMID: 34528948 DOI: 10.1039/d1ay00520k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Exponential amplification reaction (EXPAR) has attracted much attention due to its simple primers and high amplification efficiency, but its applications are hindered by severe non-specificity amplification. Convenient exogenous chemical modification methods modified the entire template while inhibiting both non-specific and specific amplification. In this paper, we proposed a new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of EXPAR. We phosphorothioated several bases where the sequence was prone to form transient intermolecular 3'-end hybridization, thereby inhibiting the non-specific interactions and preventing the extension of templates by DNA polymerase. The melting temperature (Tm) curve and density functional theory (DFT) proved that the stability of hydrogen bonds between phosphorothioated bases did decrease. Benefitting from this strategy, the detection limit had been improved by 3 orders of magnitude. Moreover, due to the antioxidation property of phosphorothioate, this strategy showed good stability in serum, reflecting its excellent prospects in clinical sampling and detection.
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Affiliation(s)
- Jikai Mao
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Shiyi Tang
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Sijia Liang
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
| | - Wufan Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yanlei Kang
- Zhejiang Province Key Laboratory of Smart Management & Application of Modern Agricultural Resources, School of Information Engineering, Huzhou University, Huzhou, 313000, Zhejiang Province, China
| | - Jianbo Cheng
- Yantai Univ, Sch Chem & Chem Engn, Lab Theoret & Computat Chem, Yantai 264005, China
| | - Dongdong Yu
- Hospital of Zhejiang University, Zhejiang University, Hangzhou 310000, China
| | - Jie Chen
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Jingan Lou
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Hong Zhao
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, 310052, China
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
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Bertucci A, Porchetta A, Del Grosso E, Patiño T, Idili A, Ricci F. Protein‐Controlled Actuation of Dynamic Nucleic Acid Networks by Using Synthetic DNA Translators**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandro Bertucci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Tania Patiño
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Andrea Idili
- Catalan Institute of Nanoscience and Nanotechnology (ICN2) Campus UAB Bellaterra 08193 Barcelona Spain
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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Bertucci A, Porchetta A, Del Grosso E, Patiño T, Idili A, Ricci F. Protein-Controlled Actuation of Dynamic Nucleic Acid Networks by Using Synthetic DNA Translators*. Angew Chem Int Ed Engl 2020; 59:20577-20581. [PMID: 32737920 DOI: 10.1002/anie.202008553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/22/2020] [Indexed: 12/20/2022]
Abstract
Integrating dynamic DNA nanotechnology with protein-controlled actuation will expand our ability to process molecular information. We have developed a strategy to actuate strand displacement reactions using DNA-binding proteins by engineering synthetic DNA translators that convert specific protein-binding events into trigger inputs through a programmed conformational change. We have constructed synthetic DNA networks responsive to two different DNA-binding proteins, TATA-binding protein and Myc-Max, and demonstrated multi-input activation of strand displacement reactions. We achieved protein-controlled regulation of a synthetic RNA and of an enzyme through artificial DNA-based communication, showing the potential of our molecular system in performing further programmable tasks.
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Affiliation(s)
- Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Andrea Idili
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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Robert A. Welch Award in Chemistry: A. Bax / Norman Hackerman Award in Chemical Research: J. D. Rimer / University Cup: X. C. Le. Angew Chem Int Ed Engl 2019; 58:1245. [PMID: 30548906 DOI: 10.1002/anie.201813596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Robert A. Welch Award in Chemistry für Adriaan Bax / Norman Hackerman Award in Chemical Research für Jeffrey D. Rimer / University Cup für X. Chris Le. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201813596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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