1
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Yan H, Wen Y, Tian Z, Hart N, Han S, Hughes SJ, Zeng Y. A one-pot isothermal Cas12-based assay for the sensitive detection of microRNAs. Nat Biomed Eng 2023; 7:1583-1601. [PMID: 37106152 PMCID: PMC11108682 DOI: 10.1038/s41551-023-01033-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 03/29/2023] [Indexed: 04/29/2023]
Abstract
The use of microRNAs as clinical cancer biomarkers is hindered by the absence of accurate, fast and inexpensive assays for their detection in biofluids. Here we report a one-step and one-pot isothermal assay that leverages rolling-circle amplification and the endonuclease Cas12a for the accurate detection of specific miRNAs. The assay exploits the cis-cleavage activity of Cas12a to enable exponential rolling-circle amplification of target sequences and its trans-cleavage activity for their detection and for signal amplification. In plasma from patients with pancreatic ductal adenocarcinoma, the assay detected the miRNAs miR-21, miR-196a, miR-451a and miR-1246 in extracellular vesicles at single-digit femtomolar concentrations with single-nucleotide specificity. The assay is rapid (sample-to-answer times ranged from 20 min to 3 h), does not require specialized instrumentation and is compatible with a smartphone-based fluorescence detection and with the lateral-flow format for visual readouts. Simple assays for the detection of miRNAs in blood may aid the development of miRNAs as biomarkers for the diagnosis and prognosis of cancers.
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Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Yunjie Wen
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Nathan Hart
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Song Han
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Steven J Hughes
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA.
- University of Florida Health Cancer Center, Gainesville, FL, USA.
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2
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Quazi MZ, Hwang J, Song Y, Park N. Hydrogel-Based Biosensors for Effective Therapeutics. Gels 2023; 9:545. [PMID: 37504424 PMCID: PMC10378974 DOI: 10.3390/gels9070545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Nanotechnology and polymer engineering are navigating toward new developments to control and overcome complex problems. In the last few decades, polymer engineering has received researchers' attention and similarly, polymeric network-engineered structures have been vastly studied. Prior to therapeutic application, early and rapid detection analyses are critical. Therefore, developing hydrogel-based sensors to manage the acute expression of diseases and malignancies to devise therapeutic approaches demands advanced nanoengineering. However, nano-therapeutics have emerged as an alternative approach to tackling strenuous diseases. Similarly, sensing applications for multiple kinds of analytes in water-based environments and other media are gaining wide interest. It has also been observed that these functional roles can be used as alternative approaches to the detection of a wide range of biomolecules and pathogenic proteins. Moreover, hydrogels have emerged as a three-dimensional (3D) polymeric network that consists of hydrophilic natural or synthetic polymers with multidimensional dynamics. The resemblance of hydrogels to tissue structure makes them more unique to study inquisitively. Preceding studies have shown a vast spectrum of synthetic and natural polymer applications in the field of biotechnology and molecular diagnostics. This review explores recent studies on synthetic and natural polymers engineered hydrogel-based biosensors and their applications in multipurpose diagnostics and therapeutics. We review the latest studies on hydrogel-engineered biosensors, exclusively DNA-based and DNA hydrogel-fabricated biosensors.
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Affiliation(s)
- Mohzibudin Z Quazi
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Jimin Hwang
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Youngseo Song
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
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3
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Li C, Wang Y, Li PF, Fu Q. Construction of rolling circle amplification products-based pure nucleic acid nanostructures for biomedical applications. Acta Biomater 2023; 160:1-13. [PMID: 36764595 DOI: 10.1016/j.actbio.2023.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Nucleic acid nanomaterials with good biocompatibility, biodegradability, and programmability have important applications in biomedical field. Nucleic acid nanomaterials are usually combined with some inorganic nanomaterials to improve their biological stability. However, undefined toxic side effects of composite nanocarriers hamper their application in vivo. As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. RCA products with different functional parts can be customized by changing the sequence of the circular template, thereby generating complex multifunctional DNA nanostructures, such as DNA nanowire, nanoflower, origami, nanotube, nanoribbon, etc. More importantly, RCA products as nonnicked building blocks can enhance the biostability of DNA nanostructures, especially in vivo. These RCA products-based nucleic acid nanostructures can be used as scaffolds or nanocarriers to interact or load with metal nanoparticles, proteins, lipids, cationic polymers, therapeutic nucleic acids or drugs, etc. This paper reviews the assembly strategies of RCA based DNA nanostructures with different shape and their applications in biosensing, bioimaging and biomedicine. Finally, the development prospects of the nucleic acid nanomaterials in clinical diagnosis and treatment of diseases are described. STATEMENT OF SIGNIFICANCE: As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. This paper reviews the construction of various shapes of pure nucleic acid nanomaterials based on RCA products and their applications in biosensing, bioimaging and biomedicine. This will promote the development of biocompatible DNA nanovehicles and their further application in living systems, including bioimaging, molecular detection, disease diagnosis and drug delivery, finally producing a significant impact in the field of nanotechnology and nanomedicine.
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Affiliation(s)
- Congcong Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Qinrui Fu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
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4
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Chen H, Zhuang Z, Chen Y, Qiu C, Qin Y, Tan C, Tan Y, Jiang Y. A universal platform for one-pot detection of circulating non-coding RNA combining CRISPR-Cas12a and branched rolling circle amplification. Anal Chim Acta 2023; 1246:340896. [PMID: 36764778 DOI: 10.1016/j.aca.2023.340896] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/02/2023] [Accepted: 01/24/2023] [Indexed: 01/26/2023]
Abstract
Multiple circulating non-coding RNAs (ncRNAs) in serum may serve as vital biomarkers for use in diagnosing early-stage colorectal cancer (CRC). Herein, a universal platform for one-pot detection of CRC-related ncRNAs was developed based on branched rolling circle amplification and CRISPR-Cas12a (BRCACas). For the implementation of the method, primers incorporating ncRNA sequences of circulating CRC-associated RNAs (piRNA or miRNA) were designed that could specifically hybridize with circular probes to initiate the BRCA process. Thereafter, the generation of dendritic DNA products triggered Cas12a trans-cleavage activity to elicit a fluorescent signal. The proposed method, combining high BRCA reaction efficiency with powerful Cas12a trans-cleavage activity, provided greatly enhanced detection sensitivity, as reflected by limits of detection (LODs) for model piRNA (piR-54265) and model miRNA (miR21) of 0.76 fM and 0.87 fM, respectively. Notably, the proposed BRCACas platform, assaying two different types of CRC-associated ncRNAs in patient samples, produced consistent results with the conventional reverse transcription-quantitative PCR (RT-qPCR) method. Therefore, the one-pot, isothermal, and specific BRCACas platform provided excellent performance, thus demonstrating its promise as a rapid, adaptable, and practical diagnostic/prognostic cancer screening method.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China; Department of Chemistry, Tsinghua University, Beijing, 100084, PR China
| | - Zhiyuan Zhuang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Yan Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Cheng Qiu
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, 518055, PR China
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China; Department of Chemistry, Tsinghua University, Beijing, 100084, PR China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China; Department of Chemistry, Tsinghua University, Beijing, 100084, PR China.
| | - Yuyang Jiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, PR China
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5
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Dong M, Tang Z, Hicks S, Guan W. Rolling Circle Amplification-Coupled Glass Nanopore Counting of Mild Traumatic Brain Injury-Related Salivary miRNAs. Anal Chem 2022; 94:3865-3871. [PMID: 35192325 DOI: 10.1021/acs.analchem.1c04781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mild traumatic brain injury (mTBI) could be underdiagnosed and underreported due to the delayed onset of symptoms and the conventional subjective assessment. Recent studies have suggested that salivary microRNAs (miRNAs) could be reliable biomarkers for objective mTBI diagnosis. In this work, we demonstrated a rolling circle amplification (RCA)-coupled resistive pulse-counting platform for profiling mTBI-related miRNAs, using easy-to-fabricate large glass nanopores (200 nm diameter). The method relies on the linear and specific elongation of the miRNA to a much larger RCA product, which the large glass nanopore can digitally count with a high signal-to-noise ratio. We developed and validated the RCA assay against let-7a, miR-30e, and miR-21. We demonstrated the quantification capability of this large glass nanopore counting platform for purified miRNAs as well as miRNAs in salivary total RNA background. Finally, we quantitatively evaluated the performance of profiling each individual miRNAs in a mixed analyte. Our results showed that the RCA-coupled large glass nanopore counting provides a promising and accessible alternative toward the clinical diagnosis of mTBI using salivary miRNAs.
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Affiliation(s)
- Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Steven Hicks
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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6
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Radfar S, Ghanbari R, Attaripour Isfahani A, Rezaei H, Kheirollahi M. A novel signal amplification tag to develop rapid and sensitive aptamer-based biosensors. Bioelectrochemistry 2022; 145:108087. [DOI: 10.1016/j.bioelechem.2022.108087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
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7
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Yang Y, Wang W, Liu H, Tong L, Mu X, Chen Z, Tang B. Sensitive Quantification of MicroRNA in Blood through Multi‐amplification Toehold‐Mediated DNA‐Strand‐Displacement Paper‐Spray Mass Spectrometry (TSD‐PS MS). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yanmei Yang
- College of Chemistry Chemical Engineering and Materials Science Key Laboratory of Molecular and Nano Probes Ministry of Education Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Institute of Molecular and Nano Science Shandong Normal University Jinan 250014 P. R. China
| | - Weiqing Wang
- College of Chemistry Chemical Engineering and Materials Science Key Laboratory of Molecular and Nano Probes Ministry of Education Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Institute of Molecular and Nano Science Shandong Normal University Jinan 250014 P. R. China
| | - Huimin Liu
- College of Chemistry Chemical Engineering and Materials Science Key Laboratory of Molecular and Nano Probes Ministry of Education Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Institute of Molecular and Nano Science Shandong Normal University Jinan 250014 P. R. China
| | - Lili Tong
- College of Chemistry Chemical Engineering and Materials Science Key Laboratory of Molecular and Nano Probes Ministry of Education Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Institute of Molecular and Nano Science Shandong Normal University Jinan 250014 P. R. China
| | - Xiaoyan Mu
- College of Chemistry Chemical Engineering and Materials Science Key Laboratory of Molecular and Nano Probes Ministry of Education Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Institute of Molecular and Nano Science Shandong Normal University Jinan 250014 P. R. China
| | - Zhenzhen Chen
- College of Chemistry Chemical Engineering and Materials Science Key Laboratory of Molecular and Nano Probes Ministry of Education Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Institute of Molecular and Nano Science Shandong Normal University Jinan 250014 P. R. China
| | - Bo Tang
- College of Chemistry Chemical Engineering and Materials Science Key Laboratory of Molecular and Nano Probes Ministry of Education Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong Institute of Molecular and Nano Science Shandong Normal University Jinan 250014 P. R. China
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8
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Yang Y, Wang W, Liu H, Tong L, Mu X, Chen Z, Tang B. Sensitive Quantification of MicroRNA in Blood through Multi-amplification Toehold-Mediated DNA-Strand-Displacement Paper-Spray Mass Spectrometry (TSD-PS MS). Angew Chem Int Ed Engl 2021; 61:e202113051. [PMID: 34881475 DOI: 10.1002/anie.202113051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Indexed: 11/07/2022]
Abstract
Accurate quantification of disease-signature microRNAs (miRNAs) in biomedical samples is in high demand for clinical diagnosis but still challenging because of low miRNAs abundance and complicating interferences in the milieus. Here, we report a multi-amplification strategy for blood miRNAs analysis based on paper-spray mass spectrometry (PS MS). A toehold-mediated DNA-strand-displacement reaction (TSD) is employed to amplify the signal chain and to ensure the specificity. The signal chain is then cleaved by UV to release signal molecules for detection. Moreover, paper spray can efficiently filter out the interfering substances in blood and further enhances the detecting sensitivity. This concept is successfully demonstrated in the prototype detection of a cancer biomarker miRNA-141 in blood and serum. The proposed TSD-PS MS approach provides an efficient way for sensitive detection of oligonucleotides with low concentration in complicating milieus.
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Affiliation(s)
- Yanmei Yang
- Shandong Normal University, College of Chemistry, 80, CHINA
| | - Weiqing Wang
- Shandong Normal University, College of Chemistry, CHINA
| | - Huimin Liu
- Shandong Normal University, College of Chemistry, CHINA
| | - Lili Tong
- Shandong Normal University, College of Chmistry, CHINA
| | - Xiaoyan Mu
- Shandong Normal University, College of Chemistry, CHINA
| | - Zhenzhen Chen
- Shandong Normal University, College of Chemistry, CHINA
| | - Bo Tang
- Shandong Normal University, Chemistry, No.88 Wenhua East Road, 250014, Jinan, CHINA
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9
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Li M, Li D, Huang G, Zhou L, Wen Q, Zhu W, Pan H. Signal-on electrochemical DNA (E-DNA) sensor for accurate quantification of nicking-assisted rolling circle amplification (N-RCA) products with attomolar sensitivity. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5679-5684. [PMID: 34812441 DOI: 10.1039/d1ay01664d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rolling circle amplification (RCA) has become an increasingly important amplification technique in nucleic acid analysis, immunoassay, and molecular diagnosis due to its high specificity and sensitivity. However, the accurate quantification of RCA products via the extensively used fluorescent signaling method has been challenged primarily by the non-specific and sequence-independent binding of the fluorescent dyes to DNA. Here, we have developed a signal-on E-DNA sensor for accurate quantification of the RCA products with high specificity and sensitivity. A restriction enzyme was introduced to cleave the long tandem repeat sequences generated in the RCA reaction into many short monomers. The short monomers were then used as secondary targets to trigger the E-DNA sensor to produce an amplified redox current and thus the resulting RCA products were detected. The method was successfully applied to the detection of miR-7a with high specificity and the detection limit was as low as 0.59 fM.
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Affiliation(s)
- Mengmeng Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China.
| | - Dandan Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China.
| | - Guidan Huang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China.
| | - Linying Zhou
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China.
| | - Qilin Wen
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China.
| | - Wenyuan Zhu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China.
| | - Hongcheng Pan
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China.
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10
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Recent Advancements in Polythiophene-Based Materials and their Biomedical, Geno Sensor and DNA Detection. Int J Mol Sci 2021; 22:ijms22136850. [PMID: 34202199 PMCID: PMC8268102 DOI: 10.3390/ijms22136850] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/20/2021] [Accepted: 06/20/2021] [Indexed: 11/17/2022] Open
Abstract
In this review, the unique properties of intrinsically conducting polymer (ICP) in biomedical engineering fields are summarized. Polythiophene and its valuable derivatives are known as potent materials that can broadly be applied in biosensors, DNA, and gene delivery applications. Moreover, this material plays a basic role in curing and promoting anti-HIV drugs. Some of the thiophene’s derivatives were chosen for different experiments and investigations to study their behavior and effects while binding with different materials and establishing new compounds. Many methods were considered for electrode coating and the conversion of thiophene to different monomers to improve their functions and to use them for a new generation of novel medical usages. It is believed that polythiophenes and their derivatives can be used in the future as a substitute for many old-fashioned ways of creating chemical biosensors polymeric materials and also drugs with lower side effects yet having a more effective response. It can be noted that syncing biochemistry with biomedical engineering will lead to a new generation of science, especially one that involves high-efficiency polymers. Therefore, since polythiophene can be customized with many derivatives, some of the novel combinations are covered in this review.
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11
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Lai W, Xiao M, Yang H, Li L, Fan C, Pei H. Circularized blocker-displacement amplification for multiplex detection of rare DNA variants. Chem Commun (Camb) 2021; 56:12331-12334. [PMID: 32959033 DOI: 10.1039/d0cc05283c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A superselective isothermal amplification technique, termed circularized blocker-displacement amplification, was developed for multiplex analysis of rare DNA variants.
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Affiliation(s)
- Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Haihong Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
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12
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Loibl N, Arenz C, Seitz O. Monitoring Dicer-Mediated miRNA-21 Maturation and Ago2 Loading by a Dual-Colour FIT PNA Probe Set. Chembiochem 2020; 21:2527-2532. [PMID: 32270536 PMCID: PMC7496889 DOI: 10.1002/cbic.202000173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The inhibition of micro RNA (miRNA) maturation by Dicer and loading matured miRNAs into the RNA-induced silencing complex (RISC) is envisioned as a modality for treatment of cancer. Existing methods for evaluating maturation either focus on the conversion of modified precursors or detect mature miRNA. Whereas the former is not applicable to native pre-miRNA, the latter approach underestimates maturation when both nonmatured and matured miRNA molecules are subject to cleavage. We present a set of two orthogonally labelled FIT PNA probes that distinguish between cleaved pre-miRNA and the mature miRNA duplex. The probes allow Dicer-mediated miR21 maturation to be monitored and Ago2-mediated unwinding of the miR21 duplex to be assayed. A two-channel fluorescence readout enables measurement in real-time without the need for specialized instrumentation or further enzyme mediated amplification.
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Affiliation(s)
- Natalia Loibl
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Christoph Arenz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
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13
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Cao H, Zhou X, Zeng Y. Microfluidic Exponential Rolling Circle Amplification for Sensitive microRNA Detection Directly from Biological Samples. SENSORS AND ACTUATORS. B, CHEMICAL 2019; 279:447-457. [PMID: 30533973 PMCID: PMC6284813 DOI: 10.1016/j.snb.2018.09.121] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
There is an urgent need of sensitive bioanalytical platforms for sensitive and precise quantification of low-abundance microRNA targets in complex biological samples, including liquid biopsies of tumors. Many of current miRNA biosensing methods require laborious sample pretreatment procedures, including extraction of total RNA, which largely limits their biomedical and clinical applications. Herein we developed an integrated Microfluidic Exponential Rolling Circle Amplification (MERCA) platform for sensitive and specific detection of microRNAs directly in minimally processed samples. The MERCA system integrates and streamlines solid-phase miRNA isolation, miRNA-adapter ligation, and a dualphase exponential rolling circle amplification (eRCA) assay in one analytical workflow. By marrying the advantages of microfluidics in leveraging bioassay performance with the high sensitivity of eRCA, our method affords a remarkably low limit of detection at <10 zeptomole levels, with the ability to discriminate single-nucleotide difference. Using the MERCA chip, we demonstrated quantitative detection of miRNAs in total RNA, raw cell lysate, and cellderived exosomes. Comparing with the parallel TaqMan RT-qPCR measurements verified the adaptability of the MERCA system for detection of miRNA biomarkers in complex biological materials. In particular, high sensitivity of our method enables direct detection of low-level exosomal miRNAs in as few as 2 × 106 exosomes. Such analytical capability immediately addresses the unmet challenge in sample consumption, a key setback in clinical development of exosome-based liquid biopsies. Therefore, the MERCA would provide a useful platform to facilitate miRNA analysis in broad biological and clinical applications.
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Affiliation(s)
- Hongmei Cao
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| | - Xin Zhou
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| | - Yong Zeng
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
- University of Kansas Cancer Center, Kansas City, KS 66160
- Corresponding authors: , Fax: 785-864-5396
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14
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Chen X, Wang Y, Zhang J, Zhang Y. DNA concatemer-silver nanoparticles as a signal probe for electrochemical prostate-specific antigen detection. Analyst 2019; 144:6313-6320. [DOI: 10.1039/c9an01484e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A ultrasensitive electrochemical detection of prostate-specific antigen was reported based on hybridization chain reaction amplifying silver nanoparticles response signal.
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Affiliation(s)
- Xi Chen
- College of Chemistry and Materials Science
- Anhui Key Laboratory of Chem-Biosensing
- Anhui Normal University
- Wuhu 241000
- People's Republic of China
| | - Ya Wang
- College of Chemistry and Materials Science
- Anhui Key Laboratory of Chem-Biosensing
- Anhui Normal University
- Wuhu 241000
- People's Republic of China
| | - Junjun Zhang
- College of Chemistry and Materials Science
- Anhui Key Laboratory of Chem-Biosensing
- Anhui Normal University
- Wuhu 241000
- People's Republic of China
| | - Yuzhong Zhang
- College of Chemistry and Materials Science
- Anhui Key Laboratory of Chem-Biosensing
- Anhui Normal University
- Wuhu 241000
- People's Republic of China
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15
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Ultrasensitive assay based on a combined cascade amplification by nicking-mediated rolling circle amplification and symmetric strand-displacement amplification. Anal Chim Acta 2019; 1047:172-178. [DOI: 10.1016/j.aca.2018.10.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/31/2018] [Accepted: 10/03/2018] [Indexed: 01/05/2023]
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16
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Yang Y, Zhong S, Wang K, Huang J. Gold nanoparticle based fluorescent oligonucleotide probes for imaging and therapy in living systems. Analyst 2019; 144:1052-1072. [DOI: 10.1039/c8an02070a] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gold nanoparticles (AuNPs) with unique physical and chemical properties have become an integral part of research in nanoscience.
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Affiliation(s)
- Yanjing Yang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- PR China
- State Key Laboratory of Chemo/Biosensing and Chemometrics
| | - Shian Zhong
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- PR China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
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17
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Wei K, Zhao J, Qin Y, Li S, Huang Y, Zhao S. A novel multiplex signal amplification strategy based on microchip electrophoresis platform for the improved separation and detection of microRNAs. Talanta 2018; 189:437-441. [DOI: 10.1016/j.talanta.2018.07.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 01/18/2023]
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18
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Wang K, Zhai FH, He MQ, Wang J, Yu YL, He RH. A simple enzyme-assisted cascade amplification strategy for ultrasensitive and label-free detection of DNA. Anal Bioanal Chem 2018; 411:4569-4576. [DOI: 10.1007/s00216-018-1422-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023]
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19
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Nicking-enhanced rolling circle amplification for sensitive fluorescent detection of cancer-related microRNAs. Anal Bioanal Chem 2018; 410:6819-6826. [PMID: 30066196 DOI: 10.1007/s00216-018-1277-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/02/2018] [Accepted: 07/16/2018] [Indexed: 01/23/2023]
Abstract
In this study, a biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) was proposed for the highly sensitive detection of cancer-related let-7a microRNA (miRNA). The sensing system consists of a padlock probe (PP), which contains a target recognition sequence and two binding sites for nicking endonuclease (NEase), and molecular beacon (MB) as reporting molecule. Upon hybridization with let-7a, the PP can be circularized by ligase. Then, the miRNA acted as polymerization primer to initiate rolling circle amplification (RCA). With the assistance of NEase, RCA products can be nicked on the cyclized PP and are displaced during the subsequent duplication process, generating numerous nicked fragments (NFs). These NFs not only induce another RCA reaction but also open the molecular beacons (MBs) via hybridization, leading to significantly amplified fluorescence signal. Under the optimized conditions, this method exhibits high sensitivity toward target miRNA let-7a with a detection limit of as low as 10 pM, a dynamic range of three orders of magnitude is achieved, and its family member is easily distinguished even with only one mismatched base. Meanwhile, it displays good recovery and satisfactory reproducibility in fetal bovine serum (FBS). Therefore, these merits endow the newly proposed N-RCA strategy with powerful implications for miRNA detection. Graphical abstract A biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) for the highly sensitive detection of cancer-related let-7a microRNA.
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20
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Rasouli E, Shahnavaz Z, Basirun WJ, Rezayi M, Avan A, Ghayour-Mobarhan M, Khandanlou R, Johan MR. Advancements in electrochemical DNA sensor for detection of human papilloma virus - A review. Anal Biochem 2018; 556:136-144. [PMID: 29981317 DOI: 10.1016/j.ab.2018.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/29/2022]
Abstract
Human papillomavirus (HPV) is one of the most common sexually transmitted disease, transmitted through intimate skin contact or mucosal membrane. The HPV virus consists of a double-stranded circular DNA and the role of HPV virus in cervical cancer has been studied extensively. Thus it is critical to develop rapid identification method for early detection of the virus. A portable biosensing device could give rapid and reliable results for the identification and quantitative determination of the virus. The fabrication of electrochemical biosensors is one of the current techniques utilized to achieve this aim. In such electrochemical biosensors, a single-strand DNA is immobilized onto an electrically conducting surface and the changes in electrical parameters due to the hybridization on the electrode surface are measured. This review covers the recent developments in electrochemical DNA biosensors for the detection of HPV virus. Due to the several advantages of electrochemical DNA biosensors, their applications have witnessed an increased interest and research focus nowadays.
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Affiliation(s)
- Elisa Rasouli
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Zohreh Shahnavaz
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Wan Jefrey Basirun
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Majid Rezayi
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Ghayour-Mobarhan
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Roshanak Khandanlou
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University, 3350, Ballarat, Australia.
| | - Mohd Rafie Johan
- Nanotechnology & Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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21
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Deng X, Qin S, Chen Y, Liu HY, Yuan E, Deng H, Liu SM. B-RCA revealed circulating miR-33a/b associates with serum cholesterol in type 2 diabetes patients at high risk of ASCVD. Diabetes Res Clin Pract 2018; 140:191-199. [PMID: 29601916 DOI: 10.1016/j.diabres.2018.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/23/2018] [Accepted: 03/09/2018] [Indexed: 10/17/2022]
Abstract
AIMS Type 2 diabetes (T2D) is a complex metabolic disease with high incidence throughout the world. Dyslipidemia is the leading cause of atherosclerotic cardiovascular diseases (ASCVD) in T2D patients. hsa-miR-33 (miR-33) serves as a regulator in lipid metabolism. We hypothesized that blood miR-33 associates with serum lipids in T2D patients at high risk of ASCVD events. METHODS We developed a branched rolling circle amplification (B-RCA) method and assessed its sensitivity and specificity with miR-33a/b standards by traditional TaqMan assay. Circulating miR-33a/b level was then determined with B-RCA in 30 T2D patients at high risk for developing ASCVD and 33 healthy controls. Pearson correlation coefficient was used to evaluate the correlation between circulating miR-33a/b and serum cholesterol. RESULTS Compared with TaqMan assay, B-RCA method showed a similar specificity and a 100-fold higher sensitivity for miR-33a detection. Circulating miR-33a/b level is positively correlated with serum total cholesterol (TC) (r = 0.364, p = 0.048) and low-density lipoprotein cholesterol (LDL-C) (r = 0.383, p = 0.037) in T2D patients at high risk for developing ASCVD. CONCLUSIONS Our B-RCA method provided an alternative strategy with specificity and high sensitivity for circulating miRNAs detection, and the results demonstrated that miR-33a/b might play an important role in cholesterol regulation.
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Affiliation(s)
- Xujing Deng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China.
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China.
| | - Huan-Yu Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China; Department of Clinical Medicine, Hubei University of Medicine, Hubei 442000, China.
| | - Erfeng Yuan
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Haohua Deng
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China.
| | - Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China.
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22
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Takahashi H, Ohkawachi M, Horio K, Kobori T, Aki T, Matsumura Y, Nakashimada Y, Okamura Y. RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection. Sci Rep 2018; 8:7770. [PMID: 29773824 PMCID: PMC5958062 DOI: 10.1038/s41598-018-26132-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3′-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes. When padlock probes are hybridized to the target RNA molecule, they are converted to the circular form by SplintR ligase. Subsequently, RNase H creates nick sites only in the hybridized RNA sequence, and single-stranded DNA is finally synthesized from the nick site by phi29 DNA polymerase. This method could specifically detect at least 10 fmol of the target RNA molecule without reverse transcription. Moreover, this method detected GFP mRNA present in 10 ng of total RNA isolated from Escherichia coli without background DNA amplification. Therefore, this method can potentially detect almost all types of RNA molecules without reverse transcription and reveal full-length sequence information.
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Affiliation(s)
- Hirokazu Takahashi
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Masahiko Ohkawachi
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Kyohei Horio
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Toshiro Kobori
- Division of Food Biotechnology, Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8642, Japan
| | - Tsunehiro Aki
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Yukihiko Matsumura
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan.,Division of Energy and Environmental Engineering, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8527, Japan
| | - Yutaka Nakashimada
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Yoshiko Okamura
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan.
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23
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Wang LJ, Ren M, Liang L, Zhang CY. Controllable fabrication of bio-bar codes for dendritically amplified sensing of human T-lymphotropic viruses. Chem Sci 2018; 9:4942-4949. [PMID: 29938021 PMCID: PMC5994793 DOI: 10.1039/c8sc01641k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
We demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA.
Human T-lymphotropic virus type II (HTLV-II) is an important type-C retrovirus, closely related to a variety of human diseases. Here, we demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA by the integration of terminal deoxynucleotidyl transferase (TdT)-catalyzed template-free polymerization extension with bio-bar-code amplification (BCA). HTLV-II DNA hybridizes with magnetic microparticle (MMP)-modified capture probe 1, forming a stable DNA duplex with a protruding 3′-hydroxylated sequence which may function as a primer to initiate the TdT-catalyzed first-step polymerization extension for the generation of a poly-thymidine (T) sequence. The resultant poly-T products may hybridize with poly-adenine (A) capture probe 2, inducing the self-assembly of multiple capture probe 2-/reporter probe-functionalized Au nanoparticles (AuNPs) onto the MMP. Subsequently, the reporter probes may act as the primers to initiate the TdT-catalyzed second-step polymerization extension, producing large numbers of G-rich DNAzymes for the generation of an enhanced chemiluminescence signal. Taking advantage of the efficient polymerization extension reaction catalyzed by TdT, the high amplification efficiency of BCA, and the intrinsically high sensitivity of G-rich DNAzyme-driven chemiluminescence, this method exhibits ultrahigh sensitivity with a limit of detection of as low as 0.50 aM and a large dynamic range of 9 orders of magnitude from 1 aM to 1 nM. Moreover, this method can be applied for the discrimination of a single-base mismatch and the measurement of HTLV-II DNA in both human serum and human T-lymphocytic leukemia cells, holding great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Ming Ren
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Li Liang
- Department of Tumor Chemotherapy and Radiation Sickness , Peking University Third Hospital , Beijing 100191 , China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
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24
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He S, Richert C. A Three‐State System Based on Branched DNA Hybrids. Chemistry 2018; 24:4562-4572. [DOI: 10.1002/chem.201705941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Shiliang He
- Institut für Organische ChemieUniversität Stuttgart 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart 70569 Stuttgart Germany
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25
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Sun Y, Deng R, Zhang K, Ren X, Zhang L, Li J. Single-cell study of the extracellular matrix effect on cell growth by in situ imaging of gene expression. Chem Sci 2017; 8:8019-8024. [PMID: 29568449 PMCID: PMC5855132 DOI: 10.1039/c7sc03880a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/01/2017] [Indexed: 12/16/2022] Open
Abstract
The effect of extracellular matrix stiffness on cell growth and the underlying molecular mechanism was investigated using an in situ single-cell imaging of gene expression method based on rolling circle amplification.
Cell behaviors are known to be regulated by the cellular microenvironment. Traditional cell-population based analysis methods need to separate cells from their extracellular matrix (ECM) and cannot resolve the heterogeneity of cell behaviors. Herein, an in situ single-cell analysis method based on rolling circle amplification was exploited to image gene expression in single cells for investigating the effect of ECM stiffness on cell growth. This method enables the simultaneous quantifying of the cell phenotype and gene expression at the single-cell level, which can help in understanding the underlying molecular mechanism of cell growth. It is found that ECM stiffness could affect cell growth via regulating the expression level of the cytoskeleton-assembly associated genes PFN1 and CFL1 and their co-expression pattern. Therefore, this single-cell analysis platform may facilitate us to tap into the study of “single-cell phenotypes” and elucidate the disease association of ECMs.
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Affiliation(s)
- Yupeng Sun
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Ruijie Deng
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Kaixiang Zhang
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Xiaojun Ren
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Ling Zhang
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Jinghong Li
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
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26
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Qi L, Xiao M, Wang X, Wang C, Wang L, Song S, Qu X, Li L, Shi J, Pei H. DNA-Encoded Raman-Active Anisotropic Nanoparticles for microRNA Detection. Anal Chem 2017; 89:9850-9856. [DOI: 10.1021/acs.analchem.7b01861] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lin Qi
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Mingshu Xiao
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Xiwei Wang
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Cheng Wang
- Department
of Nuclear Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P. R. China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Xiangmeng Qu
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Jiye Shi
- Kellogg
College, University of Oxford, Oxford OX2 6PN, U.K
| | - Hao Pei
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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27
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Li Y, Pu Q, Li J, Zhou L, Tao Y, Li Y, Yu W, Xie G. An “off-on” fluorescent switch assay for microRNA using nonenzymatic ligation-rolling circle amplification. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2475-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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28
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Xu J, Wu ZS, Shen W, Le J, Zheng T, Li H, Jia L. Programmable nanoassembly consisting of two hairpin-DNAs for p53 gene determination. Biosens Bioelectron 2017; 94:626-631. [DOI: 10.1016/j.bios.2017.03.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/16/2017] [Accepted: 03/24/2017] [Indexed: 12/12/2022]
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29
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Ma F, Liu M, Tang B, Zhang CY. Sensitive Quantification of MicroRNAs by Isothermal Helicase-Dependent Amplification. Anal Chem 2017; 89:6182-6187. [DOI: 10.1021/acs.analchem.7b01113] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Fei Ma
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Bo Tang
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical
Engineering and Materials Science, Collaborative Innovation Center
of Functionalized Probes for Chemical Imaging in Universities of Shandong,
Key Laboratory of Molecular and Nano Probes, Ministry of Education,
Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
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30
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Wang H, Wang H, Duan X, Sun Y, Wang X, Li Z. Highly sensitive and multiplexed quantification of mRNA splice variants by the direct ligation of DNA probes at the exon junction and universal PCR amplification. Chem Sci 2017; 8:3635-3640. [PMID: 28580102 PMCID: PMC5437374 DOI: 10.1039/c7sc00094d] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/01/2017] [Indexed: 02/06/2023] Open
Abstract
Alternative messenger RNA (mRNA) splicing is a basic mechanism of gene regulation. In general, reverse transcription and polymerase based primer extension limit the sensitivity and selectivity of the current detection of mRNA splice variants, respectively. Here, we show that, using the ligation of two properly designed probes at the exon junction combined with universal PCR amplification, as little as a single copy of a mRNA splice variant per cell can be accurately determined, and the dynamic range covers six orders of magnitude. Three mRNA splice variants were measured from total RNA samples derived from different cell lines. Moreover, by encoding the ligation probes with different lengths, multiplexed mRNA splice variants can be simultaneously detected in one-tube PCR amplification using electrophoretic separation.
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Affiliation(s)
- Honghong Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Hui Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Xinrui Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Yuanyuan Sun
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Xiangdong Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
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31
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32
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Liu M, Zhang Q, Chang D, Gu J, Brennan JD, Li Y. A DNAzyme Feedback Amplification Strategy for Biosensing. Angew Chem Int Ed Engl 2017; 56:6142-6146. [PMID: 28370773 DOI: 10.1002/anie.201700054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; 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 4L8 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
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33
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Magnetic beads-based DNA hybridization chain reaction amplification and DNAzyme recognition for colorimetric detection of uranyl ion in seafood. Anal Chim Acta 2017; 956:63-69. [DOI: 10.1016/j.aca.2016.12.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 11/22/2022]
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34
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Ma F, Liu WJ, Zhang Q, Zhang CY. Sensitive detection of microRNAs by duplex specific nuclease-assisted target recycling and pyrene excimer switching. Chem Commun (Camb) 2017; 53:10596-10599. [DOI: 10.1039/c7cc06290g] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Herein, we develop a sensitive fluorescence method for microRNA assay based on duplex specific nuclease-assisted target recycling and pyrene excimer switching.
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Affiliation(s)
- Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Wen-jing Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | | | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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35
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Dual-cyclical nucleic acid strand-displacement polymerization based signal amplification system for highly sensitive determination of p53 gene. Biosens Bioelectron 2016; 86:1024-1030. [DOI: 10.1016/j.bios.2016.07.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/15/2023]
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36
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Li H, Xu J, Wang Z, Wu ZS, Jia L. Increasingly branched rolling circle amplification for the cancer gene detection. Biosens Bioelectron 2016; 86:1067-1073. [DOI: 10.1016/j.bios.2016.07.095] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 11/30/2022]
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37
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Jiang HX, Liang ZZ, Ma YH, Kong DM, Hong ZY. G-quadruplex fluorescent probe-mediated real-time rolling circle amplification strategy for highly sensitive microRNA detection. Anal Chim Acta 2016; 943:114-122. [PMID: 27769370 DOI: 10.1016/j.aca.2016.09.019] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 11/24/2022]
Abstract
Real-time PCR has revolutionized PCR from qualitative to quantitative. As an isothermal DNA amplification technique, rolling circular amplification (RCA) has been demonstrated to be a versatile tool in many fields. Development of a simple, highly sensitive, and specific strategy for real-time monitoring of RCA will increase its usefulness in many fields. The strategy reported here utilized the specific fluorescence response of thioflavin T (ThT) to G-quadruplexes formed by RCA products. Such a real-time monitoring strategy works well in both traditional RCA with linear amplification efficiency and modified RCA proceeded in an exponential manner, and can be readily performed in commercially available real-time PCR instruments, thereby achieving high-throughput detection and making the proposed technique more suitable for biosensing applications. As examples, real-time RCA-based sensing platforms were designed and successfully used for quantitation of microRNA over broad linear ranges (8 orders of magnitude) with a detection limit of 4 aM (or 0.12 zmol). The feasibility of microRNA analysis in human lung cancer cells was also demonstrated. This work provides a new method for real-time monitoring of RCA by using unique nucleic acid secondary structures and their specific fluorescent probes. It has the potential to be extended to other isothermal single-stranded DNA amplification techniques.
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Affiliation(s)
- Hong-Xin Jiang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin, 300071, PR China; Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, Nankai University, Tianjin, 300071, PR China
| | - Zhen-Zhen Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; College of Life Science, Nankai University, Tianjin, 300071, PR China
| | - Yan-Hong Ma
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; College of Life Science, Nankai University, Tianjin, 300071, PR China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin, 300071, PR China; Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Zhang-Yong Hong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, PR China; College of Life Science, Nankai University, Tianjin, 300071, PR China.
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38
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Chi BZ, Liang RP, Qiu WB, Yuan YH, Qiu JD. Direct fluorescence detection of microRNA based on enzymatically engineered primer extension poly-thymine (EPEPT) reaction using copper nanoparticles as nano-dye. Biosens Bioelectron 2016; 87:216-221. [PMID: 27566394 DOI: 10.1016/j.bios.2016.08.042] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 07/31/2016] [Accepted: 08/13/2016] [Indexed: 01/03/2023]
Abstract
A new strategy based on enzymatically engineered primer extension poly-thymine (EPEPT) and nanomaterials in situ generation technology is reported for direct detection of microRNA (miRNA) in a fluorescence turn-on format using the sequential and complementary reactions catalyzed by Klenow Fragment exo- (KFexo-) and terminal deoxynucleotidyl transferase (TdTase). The short miRNA can be efficiently converted into long poly-thymine (polyT) sequences, which function as template for in situ formation of fluorescence copper nanoparticles (CuNPs) as nano-dye for detecting miRNA. The polyT-CuNPs can effectively form and emit intense red fluorescence under the 340nm excitation. For the proof of concept, microRNA-21 (miR-21) was selected as the model target to testify this strategy as a versatile assay platform. By directly using miR-21 as the primer, the simple, rapid and sensitive miRNA detection was successfully achieved with a good linearity between 1pM and 1nM and a detection limit of 100fM. Thus, the EPEPT strategy holds great potential in biochemical sensing research as an efficient and universal platform.
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Affiliation(s)
- Bao-Zhu Chi
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Ru-Ping Liang
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, China.
| | - Wei-Bin Qiu
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Yan-Hong Yuan
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Jian-Ding Qiu
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, China.
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39
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Liang WB, Yang MZ, Zhuo Y, Zheng YN, Xiong CY, Chai YQ, Yuan R. Competitive method-based electrochemiluminescent assay with protein-nucleotide conversion for ratio detection to efficiently monitor the drug resistance of cancer cells. Chem Sci 2016; 7:7094-7100. [PMID: 28451145 PMCID: PMC5355943 DOI: 10.1039/c6sc02801b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/04/2016] [Indexed: 12/29/2022] Open
Abstract
A competitive method-based electrochemiluminescent (ECL) assay with a single ECL indicator was proposed to efficiently estimate the concentration ratio of two proteins.
A simple and highly-efficient approach to monitor the expression of P-glycoprotein (P-gp) in cells was urgently needed to demonstrate the drug resistance of cancer cells. Herein, a competitive method-based electrochemiluminescent (ECL) assay with a single ECL indicator was proposed for the first time to efficiently estimate the concentration ratio of two proteins. By converting the different proteins to partially coincident nucleotide sequences via a sandwich type immunoassay on magnetic beads, the concentration ratio related ECL signals could be obtained via competitive nucleotide hybridization on an electrode surface. This method could thoroughly overcome the limitations of simultaneous ECL assays via multiple ECL indicators with inevitable cross reactions. At the same time, rolling circle amplification was employed to improve the detection performances, especially the detection limit and sensitivity. With P-gp and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as a model, the proposed ECL assay was successfully employed to monitor the drug resistance of cancer cells. Compared with conventional technologies, improved sensitivity and accuracy were achieved with a correlation coefficient of 0.9928 and a detection limit of 0.52%. Success in the establishment of the competitive method-based ECL assay offered an efficient strategy to demonstrate the concentration ratio of two proteins and a potential approach for detecting other proteins and nucleotide sequences, revealing a new avenue for ultrasensitive biomolecule diagnostics, especially in cell function research.
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Affiliation(s)
- Wen-Bin Liang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University) , Ministry of Education , College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; .,Department of Clinical Biochemistry , Laboratory Sciences , Southwest Hospital , Third Military Medical University , 30 Gaotanyan Street, Shapingba District , Chongqing 400038 , PR China
| | - Ming-Zhen Yang
- Department of Clinical Biochemistry , Laboratory Sciences , Southwest Hospital , Third Military Medical University , 30 Gaotanyan Street, Shapingba District , Chongqing 400038 , PR China
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University) , Ministry of Education , College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ;
| | - Ying-Ning Zheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University) , Ministry of Education , College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ;
| | - Cheng-Yi Xiong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University) , Ministry of Education , College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ;
| | - Ya-Qin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University) , Ministry of Education , College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ;
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University) , Ministry of Education , College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ;
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40
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Mao L, Lu Z, He N, Zhang L, Deng Y, Duan D. A new method for improving the accuracy of miRNA detection with NaYF4:Yb,Er upconversion nanoparticles. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0021-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Miao X, Wang W, Kang T, Liu J, Shiu KK, Leung CH, Ma DL. Ultrasensitive electrochemical detection of miRNA-21 by using an iridium(III) complex as catalyst. Biosens Bioelectron 2016; 86:454-458. [PMID: 27424263 DOI: 10.1016/j.bios.2016.07.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/27/2016] [Accepted: 07/01/2016] [Indexed: 11/17/2022]
Abstract
The ultrasensitive electrochemical detection of miRNA-21 was realized by using a novel redox and catalytic "all-in-one" mechanism with an iridium(III) complex as a catalyst. To construct such a sensor, a capture probe (CP) was firstly immobilized onto the gold electrode surface. In the presence of miRNA-21, a sandwiched DNA complex could form between CP and a methylene blue (MB) labeled G-rich detection probe modified onto a gold nanoparticle (AuNP) surface (DP-AuNPs). Upon addition of K(+), the structure of DP changed to a G-quadruplex. Then, the iridium(III) complex could selectively interact with the G-quadruplex, catalyzing the reduction of H2O2, which was accompanied by an electrochemical signal change using MB as an electron mediator. Under optimal conditions, the electrochemical signal of MB reduction peak was proportional to miRNA concentration in the range from 5.0 fM to 1.0 pM, with a detection limit of 1.6 fM. In addition, satisfactory results were obtained for miRNA-21 detection in human serum samples, indicating a potential application of the sensor for bioanalysis.
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Affiliation(s)
- Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Tianshu Kang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Jinbiao Liu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Kwok-Keung Shiu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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42
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Xu Y, Wang Y, Liu S, Yu J, Wang H, Guo Y, Huang J. Ultrasensitive and rapid detection of miRNA with three-way junction structure-based trigger-assisted exponential enzymatic amplification. Biosens Bioelectron 2016; 81:236-241. [DOI: 10.1016/j.bios.2016.02.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/31/2016] [Accepted: 02/13/2016] [Indexed: 11/24/2022]
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43
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Two-wheel drive-based DNA nanomachine and its sensing potential for highly sensitive analysis of cancer-related gene. Biomaterials 2016; 100:110-7. [PMID: 27254471 DOI: 10.1016/j.biomaterials.2016.05.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/20/2016] [Accepted: 05/17/2016] [Indexed: 12/16/2022]
Abstract
With the biological significance and important advances of nano-scale DNA devices, scientific activities have been directed toward developing molecular machinery. In this work, we present a novel two-wheel drive-based DNA nanomachine composed of one signaling recognition probe (SRP), one label-free recognition probe (LRP), and one driving primer (DP). Target DNA hybridization can activate LRP-based wheel driving by resorting to DP-mediated polymerization/nicking/displacement cycles. This in turn results in the accumulation of nicked strand 1 (NS1) that can initiate extended SRP-based wheel driving. As a result, the hairpin structure of SRP is stretched and pre-quenched fluorescence is restored. Meanwhile, lots of nicked strand 2 (NS2) are produced, which could hybridize perfectly with SRP and lead to further fluorescence amplification. It is worth noting that, because the nanomachine operation relies strongly on inputted target trigger, the unwanted background is completely eliminated. The detection limit of 1 pM and an excellent capability to recognize the single-base mutation were achieved. Significantly, the interrogating of target trigger extracted from cancer cells is already available, reflecting the potential for practical applications. As a proof-of-concept building, the unique analytical properties would significantly benefit the DNA nanomachines and reveal great promise in biochemical and biomedical studies.
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44
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Shi K, Dou B, Yang J, Yuan R, Xiang Y. Cascaded strand displacement for non-enzymatic target recycling amplification and label-free electronic detection of microRNA from tumor cells. Anal Chim Acta 2016; 916:1-7. [DOI: 10.1016/j.aca.2016.02.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 12/28/2022]
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45
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Ji D, Mohsen MG, Harcourt EM, Kool ET. ATP‐Releasing Nucleotides: Linking DNA Synthesis to Luciferase Signaling. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Debin Ji
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | | | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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46
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Jung IY, Lee EH, Suh AY, Lee SJ, Lee H. Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection. Anal Bioanal Chem 2016; 408:2383-406. [PMID: 26781106 DOI: 10.1007/s00216-015-9212-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/19/2015] [Accepted: 11/23/2015] [Indexed: 02/06/2023]
Abstract
Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.
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Affiliation(s)
- Il Young Jung
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Eun Hee Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Ah Young Suh
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Seung Jin Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyukjin Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea.
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47
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Khan N, Mironov G, Berezovski MV. Direct detection of endogenous MicroRNAs and their post-transcriptional modifications in cancer serum by capillary electrophoresis-mass spectrometry. Anal Bioanal Chem 2016; 408:2891-9. [DOI: 10.1007/s00216-015-9277-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/11/2015] [Accepted: 12/16/2015] [Indexed: 01/06/2023]
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48
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Hesse M, Arenz C. A Rapid and Versatile Assay for Ago2-Mediated Cleavage by Using Branched Rolling Circle Amplification. Chembiochem 2016; 17:304-7. [DOI: 10.1002/cbic.201500537] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Marlen Hesse
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Christoph Arenz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
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49
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Ji D, Mohsen MG, Harcourt EM, Kool ET. ATP-Releasing Nucleotides: Linking DNA Synthesis to Luciferase Signaling. Angew Chem Int Ed Engl 2016; 55:2087-91. [PMID: 26836342 DOI: 10.1002/anie.201509131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/20/2015] [Indexed: 12/13/2022]
Abstract
A new strategy is reported for the production of luminescence signals from DNA synthesis through the use of chimeric nucleoside tetraphosphate dimers in which ATP, rather than pyrophosphate, is the leaving group. ATP-releasing nucleotides (ARNs) were synthesized as derivatives of the four canonical nucleotides. All four derivatives are good substrates for DNA polymerase, with Km values averaging 13-fold higher than those of natural dNTPs, and kcat values within 1.5-fold of those of native nucleotides. Importantly, ARNs were found to yield very little background signal with luciferase. DNA synthesis experiments show that the ATP byproduct can be harnessed to elicit a chemiluminescence signal in the presence of luciferase. When using a polymerase together with the chimeric nucleotides, target DNAs/RNAs trigger the release of stoichiometrically large quantities of ATP, thereby allowing sensitive isothermal luminescence detection of nucleic acids as diverse as phage DNAs and short miRNAs.
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Affiliation(s)
- Debin Ji
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Emily M Harcourt
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
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50
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Yao J, Zhang Z, Zhao Y, Jing W, Zuo G. Double-stranded probe modified AuNPs for sensitive and selective detection of microRNA 30a in solution and live cell. RSC Adv 2016. [DOI: 10.1039/c6ra05131f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this article, we reported a double-stranded DNA probe modified gold nanoparticle used as both “nano-flares” and transfection agents to quantify miR-30a in solution and visualize in live cells.
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Affiliation(s)
- Juan Yao
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Zhang Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Yingze Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology
- Institute of Zoology
- Chinese Academy of Sciences
- Beijing 100101
- P. R. China
| | - Wanli Jing
- Department of Orthopaedics
- Tianjin First Center Hospital
- Tianjin 300192
- P. R. China
| | - Guowei Zuo
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
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