1
|
Ma T, Zhang Q, Zhang S, Yue D, Wang F, Ren Y, Zhang H, Wang Y, Wu Y, Liu LE, Yu F. Research progress of human key DNA and RNA methylation-related enzymes assay. Talanta 2024; 273:125872. [PMID: 38471421 DOI: 10.1016/j.talanta.2024.125872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore,it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.
Collapse
Affiliation(s)
- Tiantian Ma
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongwen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Yue
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fanting Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujie Ren
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Hengmiao Zhang
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Yinuo Wang
- Zhengzhou Foreign Language School, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
2
|
Huang Z, Wang X, Wu Z, Jiang JH. Recent Advances on DNAzyme-Based Sensing. Chem Asian J 2022; 17:e202101414. [PMID: 35156764 DOI: 10.1002/asia.202101414] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/09/2022] [Indexed: 11/08/2022]
Abstract
DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.
Collapse
Affiliation(s)
- Zhimei Huang
- Hunan University, College of Chemistry and Chemical Engineering, CHINA
| | - Xiangnan Wang
- Hunan University of Technology and Business, College of Science, CHINA
| | - Zhenkun Wu
- Hunan University, State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics and College of Chemistry and Chemical Engineering, South of Lushan Road, 410082, Changsha, CHINA
| | - Jian-Hui Jiang
- Hunan University, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering, CHINA
| |
Collapse
|
3
|
Liaqat A, Sednev MV, Stiller C, Höbartner C. RNA‐Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Maksim V. Sednev
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Carina Stiller
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| |
Collapse
|
4
|
Liaqat A, Sednev MV, Stiller C, Höbartner C. RNA-Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA. Angew Chem Int Ed Engl 2021; 60:19058-19062. [PMID: 34185947 PMCID: PMC8457104 DOI: 10.1002/anie.202106517] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/20/2021] [Indexed: 11/12/2022]
Abstract
Deoxyribozymes are emerging as modification‐specific endonucleases for the analysis of epigenetic RNA modifications. Here, we report RNA‐cleaving deoxyribozymes that differentially respond to the presence of natural methylated cytidines, 3‐methylcytidine (m3C), N4‐methylcytidine (m4C), and 5‐methylcytidine (m5C), respectively. Using in vitro selection, we found several DNA catalysts, which are selectively activated by only one of the three cytidine isomers, and display 10‐ to 30‐fold accelerated cleavage of their target m3C‐, m4C‐ or m5C‐modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The mXC‐detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m3C and m5C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites.
Collapse
Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Maksim V Sednev
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Carina Stiller
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| |
Collapse
|
5
|
Wang Y, Zhang Z, Sepich‐Poore C, Zhang L, Xiao Y, He C. LEAD‐m
6
A‐seq for Locus‐Specific Detection of
N
6
‐Methyladenosine and Quantification of Differential Methylation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202007266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yuru Wang
- Department of Biochemistry and Molecular Biology University of Chicago Chicago IL 60637 USA
- Department of Chemistry University of Chicago Chicago IL 60637 USA
| | - Zijie Zhang
- Department of Biochemistry and Molecular Biology University of Chicago Chicago IL 60637 USA
- Department of Chemistry University of Chicago Chicago IL 60637 USA
- Institute for Biophysical Dynamics University of Chicago Chicago IL 60637 USA
- Howard Hughes Medical Institute University of Chicago Chicago IL 60637 USA
| | - Caraline Sepich‐Poore
- Department of Biochemistry and Molecular Biology University of Chicago Chicago IL 60637 USA
- Department of Chemistry University of Chicago Chicago IL 60637 USA
- Institute for Biophysical Dynamics University of Chicago Chicago IL 60637 USA
- University of Chicago Medical Scientist Training Program Chicago IL 60637 USA
| | - Lisheng Zhang
- Department of Chemistry University of Chicago Chicago IL 60637 USA
- Howard Hughes Medical Institute University of Chicago Chicago IL 60637 USA
| | - Yu Xiao
- Department of Chemistry University of Chicago Chicago IL 60637 USA
| | - Chuan He
- Department of Biochemistry and Molecular Biology University of Chicago Chicago IL 60637 USA
- Department of Chemistry University of Chicago Chicago IL 60637 USA
- Institute for Biophysical Dynamics University of Chicago Chicago IL 60637 USA
- Howard Hughes Medical Institute University of Chicago Chicago IL 60637 USA
| |
Collapse
|
6
|
Wang Y, Zhang Z, Sepich-Poore C, Zhang L, Xiao Y, He C. LEAD-m 6 A-seq for Locus-Specific Detection of N 6 -Methyladenosine and Quantification of Differential Methylation. Angew Chem Int Ed Engl 2021; 60:873-880. [PMID: 32970916 PMCID: PMC7902341 DOI: 10.1002/anie.202007266] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/04/2020] [Indexed: 12/21/2022]
Abstract
N6 -methyladenosine (m6 A) is a crucial RNA chemical mark which plays important roles in various biological processes. The development of highly multiplexed, cost-effective, and easy-to-operate methodologies for locus-specific analysis of m6 A is critical for advancing our understanding of the roles of this modification. Herein, we report a method which builds upon the principle of the previously reported SELECT approach by significantly improving its efficiency and coupling it to next generation sequencing technology for high-throughput validation and detection of m6 A modification at selected sites (LEAD-m6 A-seq). Through probing cDNA extension mediated by Bst DNA polymerase at and near target cellular sites by sequencing, we evaluated m6 A modification at these sites, and estimated differential methylation levels (0-84 %) upon in vitro demethylation by the m6 A demethylase FTO with high reproducibility. We envision that this strategy can be readily used for testing a greater number of sites with a broad dynamic range and modified to study other RNA modifications.
Collapse
Affiliation(s)
- Yuru Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zijie Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Caraline Sepich-Poore
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
- University of Chicago Medical Scientist Training Program, Chicago, IL 60637, USA
| | - Lisheng Zhang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Yu Xiao
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
7
|
Liaqat A, Stiller C, Michel M, Sednev MV, Höbartner C. N6‐Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Carina Stiller
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Manuela Michel
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Maksim V. Sednev
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| |
Collapse
|
8
|
Liaqat A, Stiller C, Michel M, Sednev MV, Höbartner C. N 6 -Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes. Angew Chem Int Ed Engl 2020; 59:18627-18631. [PMID: 32681686 PMCID: PMC7589339 DOI: 10.1002/anie.202006218] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/29/2020] [Indexed: 12/15/2022]
Abstract
RNA‐cleaving deoxyribozymes can serve as selective sensors and catalysts to examine the modification state of RNA. However, site‐specific endonuclease deoxyribozymes that selectively cleave post‐transcriptionally modified RNA are extremely rare and their specificity over unmodified RNA is low. We report that the native tRNA modification N6‐isopentenyladenosine (i6A) strongly enhances the specificity and has the power to reconfigure the active site of an RNA‐cleaving deoxyribozyme. Using in vitro selection, we identified a DNA enzyme that cleaves i6A‐modified RNA at least 2500‐fold faster than unmodified RNA. Another deoxyribozyme shows unique and unprecedented behaviour by shifting its cleavage site in the presence of the i6A RNA modification. Together with deoxyribozymes that are strongly inhibited by i6A, these results highlight that post‐transcriptional RNA modifications modulate the catalytic activity of DNA in various intricate ways.
Collapse
Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Carina Stiller
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Manuela Michel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Maksim V Sednev
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| |
Collapse
|
9
|
McConnell EM, Cozma I, Morrison D, Li Y. Biosensors Made of Synthetic Functional Nucleic Acids Toward Better Human Health. Anal Chem 2019; 92:327-344. [PMID: 31656066 DOI: 10.1021/acs.analchem.9b04868] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Ioana Cozma
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1.,Department of Surgery, Division of General Surgery , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Devon Morrison
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| |
Collapse
|
10
|
Zaccara S, Ries RJ, Jaffrey SR. Reading, writing and erasing mRNA methylation. Nat Rev Mol Cell Biol 2019; 20:608-624. [PMID: 31520073 DOI: 10.1038/s41580-019-0168-5] [Citation(s) in RCA: 1566] [Impact Index Per Article: 261.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2019] [Indexed: 02/07/2023]
Abstract
RNA methylation to form N6-methyladenosine (m6A) in mRNA accounts for the most abundant mRNA internal modification and has emerged as a widespread regulatory mechanism that controls gene expression in diverse physiological processes. Transcriptome-wide m6A mapping has revealed the distribution and pattern of m6A in cellular RNAs, referred to as the epitranscriptome. These maps have revealed the specific mRNAs that are regulated by m6A, providing mechanistic links connecting m6A to cellular differentiation, cancer progression and other processes. The effects of m6A on mRNA are mediated by an expanding list of m6A readers and m6A writer-complex components, as well as potential erasers that currently have unclear relevance to m6A prevalence in the transcriptome. Here we review new and emerging methods to characterize and quantify the epitranscriptome, and we discuss new concepts - in some cases, controversies - regarding our understanding of the mechanisms and functions of m6A readers, writers and erasers.
Collapse
Affiliation(s)
- Sara Zaccara
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Ryan J Ries
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA.
| |
Collapse
|