1
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Zheng H, Munusamy S, Arora P, Jahani R, Guan X. A highly sensitive nanopore platform for measuring RNase A activity. Talanta 2024; 276:126276. [PMID: 38796995 PMCID: PMC11187776 DOI: 10.1016/j.talanta.2024.126276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
Ribonuclease A (RNase A) plays significant roles in several physiological and pathological conditions and can be used as a valuable diagnostic biomarker for human diseases such as myocardial infarction and cancer. Hence, it is of great importance to develop a rapid and cost-effective method for the highly sensitive detection of RNase A. The significance of RNase A assay is further enhanced by the growing attention from the biotechnology and pharmaceutical industries to develop RNA-based vaccines and drugs in large part as a result of the successful development of mRNA vaccines in the COVID-19 pandemic. Herein, we report a label-free method for the detection of RNase A by monitoring its proteolytic cleavage of an RNA substrate in a nanopore. The method is ultra-sensitive with the limit of detection reaching as low as 30 fg per milliliter. Furthermore, sensor selectivity and the effects of temperature, incubation time, metal ion, salt concentration on sensor sensitivity were also investigated.
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Affiliation(s)
- Haiyan Zheng
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | | | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Rana Jahani
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Xiyun Guan
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
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2
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Qin Y, Long Y, Zhou T, Luo R, Tong C, Xie Q, Wang W, Liu B. A rGO-DNAzyme assisted fluorescence method for sensitive RNase A activity assay and natural compound screening. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4298-4306. [PMID: 34473139 DOI: 10.1039/d1ay01053k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As a key regulator of human physiology and metabolic processes, ribonuclease (RNase) A can be used as an important biomarker for predicting human disease occurrence. Hence, establishing sensitive methods for tracking RNase A activity in vitro and in living cells is of great importance. Herein, we present a convenient fluorescence method assisted by reduced graphene oxide (rGO) and DNAzyme mediated fluorescence signal release for RNase A assay. The fluorescence change of the new method showed a positive linear relation with RNase A concentration in the range from 0.5 pg μL-1 to 1 ng μL-1 with a detection limit of 0.089 pg μL-1. By using this method to screen the effector of RNase A from natural compounds, the natural compound of B6 was found to stimulate RNase A activity in vitro and in vivo, the result of which was supported by the real-time imaging of RNase A in living cells. In summary, this fluorescence method with high sensitivity and specificity provides an alternative for RNase A activity assay and effector screening.
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Affiliation(s)
- Yan Qin
- College of Biology, Hunan University, Changsha, 410082, P. R. China.
- TCM and Ethnomedicine Innovation & Development International Laboratory, Innovative Material Medical Research Institute, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, P. R. China.
| | - Ying Long
- College of Biology, Hunan University, Changsha, 410082, P. R. China.
| | - Ting Zhou
- College of Biology, Hunan University, Changsha, 410082, P. R. China.
| | - Ruxin Luo
- College of Biology, Hunan University, Changsha, 410082, P. R. China.
| | - Chunyi Tong
- College of Biology, Hunan University, Changsha, 410082, P. R. China.
| | - Qian Xie
- TCM and Ethnomedicine Innovation & Development International Laboratory, Innovative Material Medical Research Institute, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, P. R. China.
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Innovative Material Medical Research Institute, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, P. R. China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha, 410082, P. R. China.
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3
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A facile and sensitive colorimetric detection for RNase A activity based on target regulated protection effect on plasmonic gold nanoparticles aggregation. Sci China Chem 2020. [DOI: 10.1007/s11426-020-9702-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Dang W, Luo R, Fan J, Long Y, Tong C, Xiao F, Xiong X, Liu B. RNase A activity analysis and imaging using label-free DNA-templated silver nanoclusters. Talanta 2020; 209:120512. [PMID: 31892040 DOI: 10.1016/j.talanta.2019.120512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/19/2019] [Accepted: 10/26/2019] [Indexed: 01/14/2023]
Abstract
A label-free, ultra-sensitive and turn-on method for detecting RNase A has been developed using enhanced DNA-templated silver nanoclusters (DNA-AgNCs) as the fluorescence probe. In this system, an RNA strand, which can perfectly hybridize with DNA template of nanocluster synthesis, was applied to lock the fluorescent signal of DNA-AgNCs by forming an RNA/DNA duplex. Meanwhile, the hybridized RNA/DNA duplex was used as the substrate of RNase A. The fluorescence signal of AgNCs was restored due to the degradation of RNA by RNase A. From the fluorescence signal change of this system caused by RNase A, it was found that the fluorescence signal showed a positive linear relation with RNase A concentration in the range from 0.2 pg/μL to 10 pg/μL with a detection limit of 0.098 pg/μL. Except for potential inhibitor screening and the kinetic study of this enzyme, this strategy was further used for monitoring dynamic change of RNase A in living cells successfully. In summary, the simple and sensitive method for RNase A assay can be hopefully used for drug screening in vitro and in vivo.
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Affiliation(s)
- Wenya Dang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ruxin Luo
- College of Biology, Hunan University, Changsha, 410082, China
| | - Jialong Fan
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ying Long
- College of Biology, Hunan University, Changsha, 410082, China
| | - Chunyi Tong
- College of Biology, Hunan University, Changsha, 410082, China
| | - Feng Xiao
- College of Biology, Hunan University, Changsha, 410082, China
| | - Xiang Xiong
- Department of Burn and Plastic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha, 410082, China.
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5
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Tong C, Hu Y, Xie Q, Zhou T, Fan J, Qin Y, Liu B, Wang W. Sensitive RNase A detection and intracellular imaging using a natural compound-assisted tetrahedral DNA nanoprobe. Chem Commun (Camb) 2020; 56:3229-3232. [DOI: 10.1039/d0cc00284d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an intracellular imaging and assay nanoplatform for RNase A using a DNA tetrahedron-based fluorescent probe as a substrate.
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Affiliation(s)
- Chunyi Tong
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Yalei Hu
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Qian Xie
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Ting Zhou
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Jialong Fan
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Yan Qin
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Bin Liu
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
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Ni J, Lin H, Yang W, Liao Y, Wang Q, Luo F, Guo L, Qiu B, Lin Z. Homogeneous Electrochemiluminescence Biosensor for the Detection of RNase A Activity and Its Inhibitor. Anal Chem 2019; 91:14751-14756. [PMID: 31651147 DOI: 10.1021/acs.analchem.9b04194] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ribonuclease A (RNase A) is increasingly considered as a biomarker for tumor diagnosis, and it is of great significance to develop an ultrasensitive, cost-effective assay for RNase A detection. Electrochemiluminescence (ECL) technology has distinctive advantages in the development of biosensors for diverse targets. However, most of the ECL biosensors require the complex process of electrode modification, which is laborious and time consuming. In this work, an immobilization-free homogeneous ECL assay was developed for the highly sensitive detection of RNase A activity for the first time. On the basis of the fact that RNase A can specifically hydrolyze RNA at the site of ribonucleotide uracil (rU), a rU-containing chimeric DNA probe is designed and labeled with Ru(bpy)32+ (act as ECL indicator). The chimeric DNA probe hardly diffuses to the surface of negatively charged indium tin oxide (ITO) electrode due to the strong electrostatic repulsion between the negatively charged DNA and ITO electrode, resulting in a weak ECL signal detected. When the RNase A is present, the chimeric DNA probe is hydrolyzed into small fragments, which contains little negative charge and can diffuse easily to the ITO electrode surface due to the decreased electrostatic repulsion. In this case, an enhanced ECL signal can be detected. Under the optimal conditions, there is a linear relationship between the ECL signal and the concentration of RNase A in the range of 0.001-0.10 ng/mL, and the detection limit is 0.2 pg/mL. In addition, the proposed ECL sensing system is also applied to detect the RNase A inhibitor, taking As3+ as an example. The proposed homogeneous ECL sensing system provides a new approach for the highly sensitive and convenient detection of RNase A as well as other ribonucleases only by redesigning a responding chimeric DNA probe.
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Affiliation(s)
- Jiancong Ni
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, College of Chemistry, Chemical Engineering and Environment , Minnan Normal University , Zhangzhou 363000 , China.,MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Hua Lin
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, College of Chemistry, Chemical Engineering and Environment , Minnan Normal University , Zhangzhou 363000 , China
| | - Weiqiang Yang
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, College of Chemistry, Chemical Engineering and Environment , Minnan Normal University , Zhangzhou 363000 , China
| | - Yuhui Liao
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital , Southern Medical University , Guangzhou 510631 , China
| | - Qingxiang Wang
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, College of Chemistry, Chemical Engineering and Environment , Minnan Normal University , Zhangzhou 363000 , China
| | - Fang Luo
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Longhua Guo
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Bin Qiu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Zhenyu Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
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7
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Thioflavin T as luminescence biosensors for nucleic acid study and RNase A activity detection. Microchem J 2019. [DOI: 10.1016/j.microc.2019.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Tong C, Zhao C, Liu B, Li B, Ai Z, Fan J, Wang W. Sensitive Detection of RNase A Activity and Collaborative Drug Screening Based on rGO and Fluorescence Probe. Anal Chem 2018; 90:2655-2661. [PMID: 29368520 DOI: 10.1021/acs.analchem.7b04429] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In addition to being an important object in theoretical and experimental studies in enzymology, RNase A also plays an important role in the development of many kinds of diseases by regulating various physiological or pathological processes, including cell growth, proliferation, differentiation, and invasion. Thus, it can be used as a useful biomarker for disease theranostics. Here, a simple, sensitive, and low-cost assay for RNase A was constructed by combining a fluorogenic substrate with reduced graphene oxide (rGO). The method with detection limit of 0.05 ng/mL was first applied for RNase A targeted drug screening, and 14 natural compounds were identified as activators of this enzyme. Then, it was applied to detect the effect of drug treatment and Hepatitis B virus (HBV) infection on RNase A activity. The results indicated that RNase A level in tumor cells was upregulated by G-10 and Chikusetsusaponin V in a concentration-dependent manner, while the average level of RNase A in the HBV infection group was significantly inhibited compared with that in the control group. Furthermore, the concentration-dependent inhibitory effect of heavy metal ions on RNase A was observed using the method and the results indicated that Ba2+, Co2+, Pb2+, As3+, and Cu2+ inhibited RNase A activity with IC50 values of 93.7 μM (Ba2+), 90.9 μM (Co2+), 110.6 μM (Pb2+), 171.5 μM (As3+), and 165.1 μM (Cu2+), respectively. In summary, considering the benefits of rapidity and high sensitivity, the method is practicable for RNase A assay in biosamples and natural compounds screening in vitro and in vivo.
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Affiliation(s)
- Chunyi Tong
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan University , Changsha 410082, China
| | - Chuan Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan University , Changsha 410082, China
| | - Bin Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan University , Changsha 410082, China
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine , Changsha 410208, China
| | - Zhaoyang Ai
- Institute of Cognition and Bio-physics Linguistics, College of FLs, Hunan University , Changsha 410082, China
| | - Jialong Fan
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan University , Changsha 410082, China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine , Changsha 410208, China
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Choi JW, Vasamsetti BMK, Kim KW, Seo SH, Lee DH, Chang SI, Choo J, Kim HY. Analysis of ribonuclease activity in sub-nanoliter droplets by label-free fluorescence measurements. Analyst 2017; 142:2610-2616. [DOI: 10.1039/c6an02724e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the results of a label-free analysis of ribonuclease activity using droplet-based microfluidics.
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Affiliation(s)
- Jae-Won Choi
- Department of Biochemistry
- Chungbuk National University
- Cheongju 28644
- Republic of Korea
| | | | - Kyu-Wan Kim
- Department of Nuclear Medicine
- College of Medicine
- Seoul National University
- Seoul 03087
- Republic of Korea
| | - Seung Hwan Seo
- Department of Biochemistry
- Chungbuk National University
- Cheongju 28644
- Republic of Korea
| | - Dong-Hun Lee
- Department of Microbiology
- Chungbuk National University
- Cheongju 28644
- Republic of Korea
- School of Biological Sciences
| | - Soo-Ik Chang
- Department of Biochemistry
- Chungbuk National University
- Cheongju 28644
- Republic of Korea
| | - Jaebum Choo
- Department of Bionano Technology
- Hanyang University
- Ansan 15588
- Republic of Korea
| | - Hak Yong Kim
- Department of Biochemistry
- Chungbuk National University
- Cheongju 28644
- Republic of Korea
- School of Biological Sciences
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10
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Duan H, Li L, Wang X, Wang Y, Li J, Luo C. Biorecognition and highly sensitive determination of Ribonuclease A with chemiluminescence sensor based on Fe3O4/multi-walled carbon nanotubes/SiO2-surface molecular imprinting polymer. RSC Adv 2015. [DOI: 10.1039/c4ra16878j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new functional material Fe3O4/MWCNTs/SiO2 was used as a supporting material to prepare SMIP for the CL determination of RNase A.
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Affiliation(s)
- Huimin Duan
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan)
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Leilei Li
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan)
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Xiaojiao Wang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan)
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Yanhui Wang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan)
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Jianbo Li
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan)
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
| | - Chuannan Luo
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan)
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- China
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Sato S, Takenaka S. Highly sensitive nuclease assays based on chemically modified DNA or RNA. SENSORS (BASEL, SWITZERLAND) 2014; 14:12437-50. [PMID: 25019631 PMCID: PMC4168492 DOI: 10.3390/s140712437] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/25/2014] [Accepted: 07/09/2014] [Indexed: 02/06/2023]
Abstract
Nucleolytic enzymes are associated with various diseases, and several methods have been developed for their detection. DNase expression is modulated in such diseases as acute myocardial infarction, transient myocardial ischemia, oral cancer, stomach cancer, and malignant lymphoma, and DNase I is used in cystic fibroma therapy. RNase is used to treat mesothelial cancer because of its antiproliferative, cytotoxic, and antineoplastic activities. Angiogenin, an angiogenic factor, is a member of the RNase A family. Angiogenin inhibitors are being developed as anticancer drugs. In this review, we describe fluorometric and electrochemical techniques for detecting DNase and RNase in disease. Oligonucleotides having fluorescence resonance energy transfer (FRET)-causing chromophores are non-fluorescent by themselves, yet become fluorescent upon cleavage by DNase or RNase. These oligonucleotides serve as a powerful tool to detect activities of these enzymes and provide a basis for drug discovery. In electrochemical techniques, ferrocenyl oligonucleotides with or without a ribonucleoside unit are used for the detection of RNase or DNase. This technique has been used to monitor blood or serum samples in several diseases associated with DNase and RNase and is unaffected by interferents in these sample types.
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Affiliation(s)
- Shinobu Sato
- Department of Applied Chemistry and Research Center for Bio-Microsensing Technology, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan.
| | - Shigeori Takenaka
- Department of Applied Chemistry and Research Center for Bio-Microsensing Technology, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan.
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