1
|
Yuan R, Bai X, Hu X, Zhang H, Hou C, Long Q, Luo Y. CATCH: high specific transcriptome-focused fusion gene variants discrimination. Chem Commun (Camb) 2022; 58:7618-7621. [PMID: 35730730 DOI: 10.1039/d2cc02660k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We develop a CRISPR-Cas13a triggered catalytic hairpin assembly (CATCH) approach for accurate and impartial identification of variants by integrating the fusion gene-selected recognition of CRISPR-Cas13a with collateral cleavage-assisted catalytic hairpin assembly amplification. This approach achieved an accuracy of 100% in a pilot experiment involving 34 clinical samples.
Collapse
Affiliation(s)
- Rui Yuan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.,Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P. R. China
| | - Xiaopeng Bai
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Xiaolin Hu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P. R. China
| | - Hong Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P. R. China.,Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Quanxin Long
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P. R. China.,Department of Clinical Laboratory, Fuling Hospital, Chongqing University, Chongqing, 408099, P. R. China.,Department of Clinical Laboratory, Jiangjin Hospital, Chongqing University, Chongqing, 402260, P. R. China
| |
Collapse
|
2
|
Gou X, Xu L, Yang S, Cheng X, Wu H, Zhang D, Shi W, Ding S, Zhang Y, Cheng W. One-Pot Identification of BCR/ABL p210 Transcript Isoforms Based on Nanocluster Beacon. ACS Sens 2021; 6:2928-2937. [PMID: 34324312 DOI: 10.1021/acssensors.1c00695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The BCR/ABLp210 fusion gene is a classic biomarker of chronic myeloid leukemia, which can be divided into e13a2 and e14a2 isoforms according to different breakpoints. These two isoforms showed distinct differences in clinical manifestation, treatment effect, and prognosis risk. Herein, a strategy based on nanocluster beacon (NCB) fluorescence was developed to identify the e13a2 and e14a2 isoforms in one-pot. Because the fluorescence of AgNCs can be activated when they are placed in proximity to the corresponding enhancer sequences, thymine-rich (T-rich) or guanine-rich (G-rich). In this work, we explored an ideal DNA-AgNCs template as an excellent molecular reporter with a high signal-to-noise ratio. After recognition with the corresponding isoforms, the AgNCs can be pulled closer to the T-rich or G-rich sequences to form a three-way junction structure and generate fluorescence with corresponding wavelengths. Therefore, by distinguishing the corresponding wavelengths of AgNCs, we successfully identified two isoforms in one tube with the limitation of 16 pM for e13a2 and 9 pM for e14a2. Moreover, this strategy also realized isoform identification in leukemia cells and newly diagnosed CML patients within 40 min, which provides a powerful tool to distinguish fusion gene subtypes at the same time.
Collapse
Affiliation(s)
- Xiaolong Gou
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lulu Xu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- The Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Suqing Yang
- Chongqing Testing & Lnspection Center for Medical Devices, Chongqing 400016, China
| | - Xiaoxue Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Decai Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Weicheng Shi
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of 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
| | - Yuhong Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of 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
| |
Collapse
|
3
|
Zhang Z, Zhang L, Wang Y, Yao J, Wang T, Weng Z, Yang L, Xie G. Ultrasensitive electrochemical biosensor for attomolar level detection of let 7a based on toehold mediated strand displacement reaction circuits and molecular beacon mediated circular strand displacement polymerization. Anal Chim Acta 2021; 1147:108-115. [PMID: 33485569 DOI: 10.1016/j.aca.2020.12.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/26/2020] [Accepted: 12/27/2020] [Indexed: 12/12/2022]
Abstract
In this study, an ultrasensitive electrochemical miRNA biosensor based on toehold mediated strand displacement reaction circuits (SDRCs) and molecular beacon mediated isothermal circular strand displacement polymerization reaction (ICSDPR) has been proposed. During the SDRCs module, the cascade strand displacement reaction induces the recycling of the target let 7a and generation of a large amount of strand A (SA). The SA recognition opens the hairpin capture probe immobilized on the gold electrode, thus, varying the distance between the redox molecules and electrode surface. The primer mediated ICSDPR is observed to further generate a large amount of SA, thus, leading to a reduction in the signal. Considering these merits, the proposed method is observed to exhibit a log-linear linearity from 10 aM to 100 pM and ultrahigh sensitivity towards let 7a down to 6.2 aM, with a capability of distinguishing the let 7a family members, thereby, providing a new electrochemical route for early cancer screening.
Collapse
Affiliation(s)
- Zhang Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China; Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Li Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Youqiang Wang
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, PR China
| | - Juan Yao
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, PR China
| | - Ting Wang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China; Department of Laboratory Medicine, Chongqing Fuling People's Hospital, Chongqing, PR China
| | - Zhi Weng
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Liu Yang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China.
| |
Collapse
|
4
|
Wang X, Tao Z. Expanding the analytical applications of nucleic acid hybridization using junction probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4931-4938. [PMID: 33043948 DOI: 10.1039/d0ay01605e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nucleic acid hybridization is crucial in target recognition with respect to in vitro and in vivo nucleic acid biosensing. Conventional linear probes and molecular beacons encounter challenges in multiplexing and specific recognition of intractable nucleic acids. Advances in nucleic acid nanotechnologies have resulted in a set of novel structural probes: junction probes (JPs), which make full use of the advantages of specificity, stability, programmability and predictability of Watson-Crick base pairing. In recent years, junction probes have been regularly implemented in constructing systems related to biosensing, synthetic biology and gene regulation. Herein, we summarize the latest advances in JP designs as potential nucleic acid biosensing systems and their expansive applications, and provide some general guidelines for developing JP based sensing strategies for implementation of such systems.
Collapse
Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China.
| | | |
Collapse
|