1
|
Lee H, Cho H, Kim J, Lee S, Yoo J, Park D, Lee G. RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids. Nucleic Acids Res 2022; 50:1801-1814. [PMID: 34788459 PMCID: PMC8886854 DOI: 10.1093/nar/gkab1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022] Open
Abstract
RNase H is involved in fundamental cellular processes and is responsible for removing the short stretch of RNA from Okazaki fragments and the long stretch of RNA from R-loops. Defects in RNase H lead to embryo lethality in mice and Aicardi-Goutieres syndrome in humans, suggesting the importance of RNase H. To date, RNase H is known to be a non-sequence-specific endonuclease, but it is not known whether it performs other functions on the structural variants of RNA:DNA hybrids. Here, we used Escherichia coli RNase H as a model, and examined its catalytic mechanism and its substrate recognition modes, using single-molecule FRET. We discovered that RNase H acts as a processive exoribonuclease on the 3' DNA overhang side but as a distributive non-sequence-specific endonuclease on the 5' DNA overhang side of RNA:DNA hybrids or on blunt-ended hybrids. The high affinity of previously unidentified double-stranded (ds) and single-stranded (ss) DNA junctions flanking RNA:DNA hybrids may help RNase H find the hybrid substrates in long genomic DNA. Our study provides new insights into the multifunctionality of RNase H, elucidating unprecedented roles of junctions and ssDNA overhang on RNA:DNA hybrids.
Collapse
Affiliation(s)
- Hyunjee Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - HyeokJin Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jooyoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sua Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungmin Yoo
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Daeho Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| |
Collapse
|
2
|
Xie Y, Zhang S, Deng T, Zhang K, Ren J, Li J. A Novel DNAzyme Signal Amplification-based Colorimetric Method for RNase H Assays. ANAL SCI 2021; 37:1675-1680. [PMID: 33162413 DOI: 10.2116/analsci.20p337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A simple visual strategy was developed for the RNase H colorimetric measurement using DNAzyme-mediated signal amplification. When RNase H was presented, the RNA strand of the duplex formed by the G-rich DNA sequence (G-Rich) and its complementary RNA sequence (cp-RNA) was digested, releasing G-Rich to form HRP-mimicking DNAzymes of the G-quadruplex/hemin complexes in the presence of hemin. These DNAzymes catalyze the oxidation reaction of the substrate of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) to produce green-color products of ABTS•-, allowing for the detection of RNase H. A horseradish peroxidase (HRP)-mimicking DNAzyme of the G-quadruplex/hemin complex was used to mediate the signal amplification in the sensing strategy, resulting in high selectivity and sensitivity. This proposed colorimetric method shows a low detection limit of 0.04 U/mL, with a detection range of 0.1 to 3 U/mL. Moreover, this colorimetric method has been successfully used for RNase H assays in complicated biosamples, such as cell lysates. These results indicate that our colorimetric method not only detects RNase H in an ideal system, but also in real samples.
Collapse
Affiliation(s)
- Ye Xie
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Sina Zhang
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Ting Deng
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Ke Zhang
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Jiali Ren
- Institute of Applied Chemistry, School of Science, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, Central South University of Forestry and Technology
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University
| |
Collapse
|
3
|
Hu Y, Xie Q, Chang L, Tao X, Tong C, Liu B, Wang W. A radar-like DNA monitor for RNase H-targeted natural compounds screening and RNase H activity in situ detection. Analyst 2021; 146:5980-5987. [PMID: 34499070 DOI: 10.1039/d1an01046h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ribonuclease H is essential for the research and development of complex pathema. The high rigidity and versatility of DNA tetrahedrons means they are often used in biosensing systems. Inspired by "radar" technology, we proposed a radar-like monitor to detect RNase H activity in vitro and in situ by integrating DNA tetrahedral elements. The structure of a radar-like monitor was self-assembled from five customized single nucleic acid strands. Four DNA strands were assembled as DNA tetrahedrons with a long strand labeled by Dabcyl (quencher) at one of the apexes, while the fifth strand (DNA-RNA heterozygous strand) was labeled with a FAM (Fluorophore) hybrid with a long strand. The fluorescence was quenched because the fluorophore and the quencher were very close. In the presence of RNase H, the RNA chain was hydrolyzed and the fluorophore released, resulting in fluorescence recovery. The radar-like monitor was used to detect the RNase H activity in vitro with a detection limit of 0.01 U mL-1. Based on the RNase H activity detection and the inhibitory effect of natural-compounds-targeting RNase H, three inhibitors were obtained among 35 compounds extracted from Panax japonicus. Therefore, the radar-like monitor was successfully used to detect RNase H activity in situ due to the long-term anti-DNase I effect of the RNA/DNA hybrid structure and DNA tetrahedrons structure. Overall, this radar-like monitor can effectively avoid false-positive signals and significantly improve the accuracy, precision, and reliability of detection. It is expected that the development of such an intelligent nano-platform will open the door to cancer diagnosis and treatment in clinical systems.
Collapse
Affiliation(s)
- Yalei Hu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, 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, China.
| | - Li Chang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410008, PR China
| | - Xueqing Tao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.
| | - Chunyi Tong
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.
| | - Bin Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, 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, China.
| |
Collapse
|
4
|
Sheet SK, Rabha M, Sen B, Patra SK, Aguan K, Khatua S. Ruthenium(II) Complex-Based G-quadruplex DNA Selective Luminescent 'Light-up' Probe for RNase H Activity Detection. Chembiochem 2021; 22:2880-2887. [PMID: 34314094 DOI: 10.1002/cbic.202100229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/03/2021] [Indexed: 12/14/2022]
Abstract
A bis-heteroleptic ruthenium(II) complex, 1[PF6 ]2 of benzothiazole amide substituted 2,2'-bipyridine ligand (bmbbipy) has been synthesized for the selective detection of G-quadruplex (GQ) DNA and luminescence-assay-based RNase H activity monitoring. Compound 1[PF6 ]2 exhibited aggregation-caused quenching (ACQ) in water. Aggregate formation was supported by DLS, UV-vis, and 1 H NMR spectroscopy results, and the morphology of aggregated particles was witnessed by SEM and TEM. 1[PF6 ]2 acted as an efficient GQ DNA-selective luminescent light-up probe over single-stranded and double-stranded DNA. The competency of 1[PF6 ]2 for selective GQ structure detection was established by PL and CD spectroscopy. For 1[PF6 ]2 , the PL light-up is exclusively due to the rigidification of the benzothiazole amide side arm in the presence of GQ-DNA. The interaction between the probe and GQ-DNA was analyzed by molecular docking analysis. The GQ structure detection capability of 1[PF6 ]2 was further applied in the luminescent 'off-on' RNase H activity detection. The assay utilized an RNA:DNA hybrid, obtained from 22AG2-RNA and 22AG2-DNA sequences. RNase H solely hydrolyzed the RNA of the RNA:DNA duplex and released G-rich 22AG2-DNA, which was detected via the PL enhancement of 1[PF6 ]2 . The selectivity of RNase H activity detection over various other restriction enzymes was also demonstrated.
Collapse
Affiliation(s)
- Sanjoy Kumar Sheet
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Monosh Rabha
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Bhaskar Sen
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Sumit Kumar Patra
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Kripamoy Aguan
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| | - Snehadrinarayan Khatua
- Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, 793022, Shillong, Meghalaya, India
| |
Collapse
|
5
|
Xie Y, Wang N, Li Y, Deng T, Li J, Zhang K, Yu R. Cyclodextrin supramolecular inclusion-enhanced pyrene excimer switching for highly selective detection of RNase H. Anal Chim Acta 2019; 1088:137-143. [PMID: 31623709 DOI: 10.1016/j.aca.2019.08.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/13/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022]
Abstract
Here, we report a novel fluorescence method for the highly selective and sensitive detection of RNase H by combining the use of a dual-pyrene-labeled DNA/RNA duplex with supramolecular inclusion-enhanced fluorescence. Initially, the probe is in the "off" state due to the rigidness of the double-stranded duplex, which separates the two pyrene units. In the presence of RNase H, the RNA strand of the DNA/RNA duplex will be hydrolyzed, and the DNA strand transforms into a hairpin structure, bringing close the two pyrene units which in turn enter the hydrophobic cavity of a γ-cyclodextrin. As a result, the pyrene excimer emission is greatly enhanced, thereby realizing the detection of RNase H activity. Under optimal conditions, RNase H detection can be achieved in the range from 0.08 to 4 U/mL, with a detection limit of 0.02 U/mL.
Collapse
Affiliation(s)
- Ye Xie
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ningning Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yulong Li
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ting Deng
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Ke Zhang
- Institute of Applied Chemistry, School of Science, College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Ruqin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| |
Collapse
|
6
|
Chang D, Chang T, Salena B, Li Y. An Unintentional Discovery of a Fluorogenic DNA Probe for Ribonuclease I. Chembiochem 2019; 21:464-468. [PMID: 31420934 DOI: 10.1002/cbic.201900455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Dingran Chang
- M.G. DeGroote Institute for Infectious Disease ResearchDepartment of Biochemistry and Biomedical SciencesDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Thomas Chang
- M.G. DeGroote Institute for Infectious Disease ResearchDepartment of Biochemistry and Biomedical SciencesDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno Salena
- Department of MedicineDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease ResearchDepartment of Biochemistry and Biomedical SciencesDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| |
Collapse
|
7
|
Tramontano E, Corona A, Menéndez-Arias L. Ribonuclease H, an unexploited target for antiviral intervention against HIV and hepatitis B virus. Antiviral Res 2019; 171:104613. [PMID: 31550450 DOI: 10.1016/j.antiviral.2019.104613] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/18/2022]
Abstract
Ribonucleases H (RNases H) are endonucleolytic enzymes, evolutionarily related to retroviral integrases, DNA transposases, resolvases and numerous nucleases. RNases H cleave RNA in RNA/DNA hybrids and their activity plays an important role in the replication of prokaryotic and eukaryotic genomes, as well as in the replication of reverse-transcribing viruses. During reverse transcription, the RNase H activity of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) degrades the viral genomic RNA to facilitate the synthesis of viral double-stranded DNA. HIV and HBV reverse transcriptases contain DNA polymerase and RNase H domains that act in a coordinated manner to produce double-stranded viral DNA. Although RNase H inhibitors have not been developed into licensed drugs, recent progress has led to the identification of a number of small molecules with inhibitory activity at low micromolar or even nanomolar concentrations. These compounds can be classified into metal-chelating active site inhibitors and allosteric inhibitors. Among them, α-hydroxytropolones, N-hydroxyisoquinolinediones and N-hydroxypyridinediones represent chemotypes active against both HIV and HBV RNases H. In this review we summarize recent developments in the field including the identification of novel RNase H inhibitors, compounds with dual inhibitory activity, broad specificity and efforts to decrease their toxicity.
Collapse
Affiliation(s)
- Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
| |
Collapse
|
8
|
Zhou Y, Zhang J, Jiang Q, Lu J. An allosteric switch-based hairpin for label-free chemiluminescence detection of ribonuclease H activity and inhibitors. Analyst 2019; 144:1420-1425. [PMID: 30607414 DOI: 10.1039/c8an02006j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To assay enzyme activities and screen its inhibitors, we demonstrated a novel label-free chemiluminescent (CL) aptasensor for the sensitive detection of RNase H activity based on hairpin technology. The specific hairpin structure was a DNA-RNA chimeric strand, which contained a streptavidin aptamer sequence and a blocked RNA sequence. RNase H could specifically recognize and cleave the RNA sequence of the DNA-RNA hybrid stem, liberating the streptavidin aptamer which could be accumulated by streptavidin-coated magnetic microspheres (SA-MP). Then the CL signal was generated due to an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxyphenyl-glyoxal (TMPG) and the guanine (G) nucleotides in the SA aptamer. This novel assay method exhibited a good linear relationship in the range of 0.1-10 U mL-1 under the optimized conditions. Our results suggested that the developed system was a promising platform for monitoring the RNase H activity and showed great potential in biomedical studies and drug screening.
Collapse
Affiliation(s)
- Ying Zhou
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
| | | | | | | |
Collapse
|
9
|
Jung Y, Lee CY, Park KS, Park HG. Target-Activated DNA Polymerase Activity for Sensitive RNase H Activity Assay. Biotechnol J 2019; 14:e1800645. [PMID: 30791223 DOI: 10.1002/biot.201800645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/11/2018] [Indexed: 01/07/2023]
Abstract
Herein, the ribonuclease H (RNase H) activity assay based on the target-activated DNA polymerase activity is described. In this method, a detection probe composed of two functional sequences, a binding site for DNA polymerase and a catalytic substrate for RNase H, serves as a key component. The detection probe, at its initial state, suppresses the DNA polymerase activity, but it becomes destabilized by RNase H, which specifically hydrolyzes RNA in RNA/DNA hybrid duplexes. As a result, DNA polymerase recovers its activity and initiates multiple primer extension reactions in a separate TaqMan probe-based signal transduction module, leading to a significantly enhanced fluorescence "turn-on" signal. This assay can detect RNase H activity as low as 0.016 U mL-1 under optimized conditions. Furthermore, its potential use for evaluating RNase H inhibitors, which have been considered potential therapeutic agents against acquired immune deficiency syndrome (AIDS), is successfully explored. In summary, this approach is quite promising for the sensitive and accurate determination of enzyme activity and inhibitor screening.
Collapse
Affiliation(s)
- Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Chang Y Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ki S Park
- Department of Biological Engineering, College of Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hyun G Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| |
Collapse
|
10
|
Liu Z, Luo D, Ren F, Ran F, Chen W, Zhang B, Wang C, Chen H, Wei J, Chen Q. Ultrasensitive fluorescent aptasensor for CRP detection based on the RNase H assisted DNA recycling signal amplification strategy. RSC Adv 2019; 9:11960-11967. [PMID: 35517011 PMCID: PMC9063470 DOI: 10.1039/c9ra01352k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/27/2022] [Accepted: 04/09/2019] [Indexed: 11/21/2022] Open
Abstract
An aptamer-based method for the ultrasensitive fluorescence detection of C-reactive protein (CRP) was developed using the ribonuclease H (RNase H) assisted DNA recycling signal amplification strategy. In this assay, CRP can specifically bind to the aptamer of CRP and the DNA chain of P1 is released from the aptamer/P1 (Ap/P1) complexes. After the addition of the fluorescence labeled (5-FAM) RNA, P1 hybridizes with fluorescence labeled RNA to form a P1/RNA double strand. When RNase H is added, the RNA with fluorescence labeling in the double strand is specifically cut into nucleotide fragments, which cannot be adsorbed on the surface of the GO, so as to generate a fluorescence signal. In the absence of CRP, fluorescence labeled RNA cannot hybridize with P1 to form double strands, which is able to directly adsorb on the surface of GO, resulting in no fluorescence signal. The detection limit is as low as 0.01 ng mL-1, with a linear dynamic range from 50 pg mL-1 to 100 ng mL-1. This sensor is able to detect CRP in spiked human serum, urine and saliva. Thus, it shows a great application prospect in disease diagnosis and prognosis.
Collapse
Affiliation(s)
- Zhongzhi Liu
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
| | - Dan Luo
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
- College of Pharmacy, Hubei University of Medicine Hubei Shiyan 442008 China
| | - Fangling Ren
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
- College of Pharmacy, Hubei University of Medicine Hubei Shiyan 442008 China
| | - Fengying Ran
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
| | - Wei Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
| | - Bingqiang Zhang
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
| | - Ceming Wang
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
| | - Hao Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
| | - Jian Wei
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
| | - Qinhua Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719 8272283
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine Hubei Shiyan 442008 China
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
An end-point method based on graphene oxide for RNase H analysis and inhibitors screening. Biosens Bioelectron 2016; 90:103-109. [PMID: 27886596 DOI: 10.1016/j.bios.2016.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/03/2016] [Accepted: 11/12/2016] [Indexed: 12/12/2022]
Abstract
As a highly conserved damage repair protein, RNase H can hydrolysis DNA-RNA heteroduplex endonucleolytically and cleave RNA-DNA junctions as well. In this study, we have developed an accurate and sensitive RNase H assay based on fluorophore-labeled chimeric substrate hydrolysis and the differential affinity of graphene oxide on RNA strand with different length. This end-point measurement method can detect RNase H in a range of 0.01 to 1 units /mL with a detection limit of 5.0×10-3 units/ mL under optimal conditions. We demonstrate the utility of the assay by screening antibiotics, resulting in the identification of gentamycin, streptomycin and kanamycin as inhibitors with IC50 of 60±5µM, 70±8µM and 300±20µM, respectively. Furthermore, the assay was reliably used to detect RNase H in complicated biosamples and found that RNase H activity in tumor cells was inhibited by gentamycin and streptomycin sulfate in a concentration-dependent manner. The average level of RNase H in serums of HBV infection group was similar to that of control group. In summary, the assay provides an alternative tool for biochemical analysis for this enzyme and indicates the feasibility of high throughput screening inhibitors of RNase H in vitro and in vivo.
Collapse
|
13
|
Peng L, Fan J, Tong C, Xie Z, Zhao C, Liu X, Zhu Y, Liu B. An ultrasensitive fluorescence method suitable for quantitative analysis of mung bean nuclease and inhibitor screening in vitro and vivo. Biosens Bioelectron 2016; 83:169-76. [DOI: 10.1016/j.bios.2016.04.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/10/2016] [Accepted: 04/18/2016] [Indexed: 02/02/2023]
|
14
|
Park KS, Lee CY, Kang KS, Park HG. Aptamer-mediated universal enzyme assay based on target-triggered DNA polymerase activity. Biosens Bioelectron 2016; 88:48-54. [PMID: 27499380 DOI: 10.1016/j.bios.2016.07.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 11/18/2022]
Abstract
We herein describe an innovative method for a universal fluorescence turn-on enzyme assay, which relies on the target enzyme-triggered DNA polymerase activity. In the first target recognition step, the target enzyme is designed to destabilize detection probe derived from an aptamer specific to DNA polymerase containing the overhang sequence and the complementary blocker DNA, which consequently leads to the recovery of DNA polymerase activity inhibited by the detection probe. This target-triggered polymerase activity is monitored in the second signal transduction step based on primer extension reaction coupled with TaqMan probe. Utilizing this design principle, we have successfully detected the activities of two model enzymes, exonuclease I and uracil DNA glycosylase with high sensitivity and selectivity. Since this strategy is composed of separated target recognition and signal transduction modules, it could be universally employed for the sensitive determination of numerous different target enzymes by simply redesigning the overhang sequence of detection probe, while keeping TaqMan probe-based signal transduction module as a universal signaling tool.
Collapse
Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea; Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea
| | - Kyoung Suk Kang
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-338, Republic of Korea.
| |
Collapse
|
15
|
Xu W, Xie Z, Tong C, Peng L, Xiao C, Liu X, Zhu Y, Liu B. A rapid and sensitive method for kinetic study and activity assay of DNase I in vitro based on a GO-quenched hairpin probe. Anal Bioanal Chem 2016; 408:3801-9. [DOI: 10.1007/s00216-016-9474-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 01/29/2023]
|
16
|
A real time S1 assay at neutral pH based on graphene oxide quenched fluorescence probe. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2015.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
17
|
A hybrid chimeric system for versatile and ultra-sensitive RNase detection. Sci Rep 2015; 5:9558. [PMID: 25828752 PMCID: PMC4381352 DOI: 10.1038/srep09558] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/11/2015] [Indexed: 12/21/2022] Open
Abstract
We developed a new versatile strategy that allows the detection of several classes of RNases (i.e., targeting ss- or ds-RNA, DNA/RNA hetero-hybrid or junctions) with higher sensitivity than existing assays. Our two-step approach consists of a DNA-RNA-DNA chimeric Hairpin Probe (cHP) conjugated to magnetic microparticles and containing a DNAzyme sequence in its terminal region, and molecular beacons for fluorescence signal generation. In the first step, the digestion of the RNA portion of the cHP sequences in presence of RNases leads to the release of multiple copies of the DNAzyme in solution. Then, after magnetic washing, each DNAzyme molecule elicits the catalytic cleavage of numerous molecular beacons, providing a strong amplification of the overall sensitivity of the assay. We successfully applied our approach to detect very low concentrations of RNase A, E. coli RNase I, and RNase H. Furthermore, we analyzed the effect of two antibiotics (penicillin and streptomycin) on RNase H activity, demonstrating the applicability of our strategy for the screening of inhibitors. Finally, we exploited our system to detect RNase activity directly in crude biological samples (i.e., blood and saliva) and in cell culture medium, highlighting its suitability as cheap and sensitive tool for the detection of RNase levels.
Collapse
|
18
|
Leung CH, Zhong HJ, He HZ, Lu L, Chan DSH, Ma DL. Luminescent oligonucleotide-based detection of enzymes involved with DNA repair. Chem Sci 2013. [DOI: 10.1039/c3sc51228b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|