1
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Adampourezare M, Nikzad B, Amini M, Sheibani N. Fluorimetric detection of DNA methylation by cerium oxide nanoparticles for early cancer diagnosis. Heliyon 2024; 10:e28695. [PMID: 38586346 PMCID: PMC10998132 DOI: 10.1016/j.heliyon.2024.e28695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
In this study, a very sensitive fluorescence nano-biosensor was developed using CeO2 nanoparticles for the rapid detection of DNA methylation. The characteristics of CeO2 nanoparticles were determined by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD) spectroscopy, UV-visible spectroscopy, and fluorescence spectroscopy. The CeO2 nanoparticles were reacted with a single-stranded DNA (ssDNA) probe, and then methylated and unmethylated target DNAs hybridized with an ssDNA probe, and the fluorescence emission was measured. Upon adding the target unmethylated and methylated ssDNA, the fluorescence intensity increased in the linear range of concentration from 2 × 10-13 - 10-18 M. The limit of detection (LOD) was 1.597 × 10-6 M for methylated DNA and 1.043 × 10-6 M for unmethylated DNA. The fluorescence emission intensity of methylated sequences was higher than of that unmethylated sequences. The fabricated DNA nanobiosensor showed a fluorescence emission at 420 nm with an excitation wavelength of 280 nm. The impact of CeO2 binding on methylated and unmethylated DNA was further demonstrated by agarose gel electrophoresis. Finally, the actual sample analysis suggested that the nanobiosensor could have practical applications for detecting methylation in the human plasma samples.
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Affiliation(s)
- Mina Adampourezare
- Research Center of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Behzad Nikzad
- Research Center of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Mojtaba Amini
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison WI 53705, USA
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2
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Chinnappan R, Mir TA, Alsalameh S, Makhzoum T, Alzhrani A, Alnajjar K, Adeeb S, Al Eman N, Ahmed Z, Shakir I, Al-Kattan K, Yaqinuddin A. Emerging Biosensing Methods to Monitor Lung Cancer Biomarkers in Biological Samples: A Comprehensive Review. Cancers (Basel) 2023; 15:3414. [PMID: 37444523 DOI: 10.3390/cancers15133414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Lung cancer is the most commonly diagnosed of all cancers and one of the leading causes of cancer deaths among men and women worldwide, causing 1.5 million deaths every year. Despite developments in cancer treatment technologies and new pharmaceutical products, high mortality and morbidity remain major challenges for researchers. More than 75% of lung cancer patients are diagnosed in advanced stages, leading to poor prognosis. Lung cancer is a multistep process associated with genetic and epigenetic abnormalities. Rapid, accurate, precise, and reliable detection of lung cancer biomarkers in biological fluids is essential for risk assessment for a given individual and mortality reduction. Traditional diagnostic tools are not sensitive enough to detect and diagnose lung cancer in the early stages. Therefore, the development of novel bioanalytical methods for early-stage screening and diagnosis is extremely important. Recently, biosensors have gained tremendous attention as an alternative to conventional methods because of their robustness, high sensitivity, inexpensiveness, and easy handling and deployment in point-of-care testing. This review provides an overview of the conventional methods currently used for lung cancer screening, classification, diagnosis, and prognosis, providing updates on research and developments in biosensor technology for the detection of lung cancer biomarkers in biological samples. Finally, it comments on recent advances and potential future challenges in the field of biosensors in the context of lung cancer diagnosis and point-of-care applications.
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Affiliation(s)
- Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Laboratory of Tissue/Organ Bioengineering & BioMEMS, Organ Transplant Centre of Excellence, Transplant Research & Innovation Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Tanveer Ahmad Mir
- Laboratory of Tissue/Organ Bioengineering & BioMEMS, Organ Transplant Centre of Excellence, Transplant Research & Innovation Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | | | - Tariq Makhzoum
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Alaa Alzhrani
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Laboratory of Tissue/Organ Bioengineering & BioMEMS, Organ Transplant Centre of Excellence, Transplant Research & Innovation Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khalid Alnajjar
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Salma Adeeb
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Noor Al Eman
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Zara Ahmed
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ismail Shakir
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Khaled Al-Kattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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3
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Liu Y, Wang X, Li Y, Wu H. An all-in-one strategy for bisulfite-free DNA methylation detection by temperature-programmed enzymatic reactions. Anal Chim Acta 2023; 1251:341001. [PMID: 36925290 DOI: 10.1016/j.aca.2023.341001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
The fragmentation and low concentration of cell-free DNA (cfDNA) pose higher challenges for the cfDNA methylation detection technologies. Conventional bisulfite conversion-based methods are inadequate for cfDNA methylation analysis due to cumbersome operation and exacerbating cfDNA degradation. Herein, we proposed temperature-programmed enzymatic reactions for cfDNA methylation analysis in a single tube. Endonuclease was used to mildly recognize DNA methylation to avoid the degradation of cfDNA. And two stages of amplification reactions significantly improved the detection sensitivity for GC-rich sequence. With vimentin as the target, the detection sensitivity was 10 copies of methylated DNA. Meanwhile, the proposed method can accurately quantify the methylation level of target sequence from 1000-fold of unmethylated DNA background. Further, the methylated vimentin gene in 20 clinical plasma samples was successfully detected. The results shown significant differences in methylation levels of the vimentin gene between healthy volunteers and colorectal cancer patients. These results lead us to believe that the proposed method has great application potential for DNA methylation analysis as a complement to bisulfite conversion-based methods.
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Affiliation(s)
- Yunlong Liu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Xiaoming Wang
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, 210009, PR China
| | - Yujiao Li
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China
| | - Haiping Wu
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China.
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4
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Shen Q, Zhang H, Huang Y, Li M, Zhao H, Yang Z, Zhao H, Liu Q, Fu Z, Di Y, Liu L, Bai H, Lv F, Chen Y, Liu Y, Wang S. Sensitive detection of single-nucleotide polymorphisms by conjugated polymers for personalized treatment of hypertension. Sci Transl Med 2023; 15:eabq5753. [PMID: 36888697 DOI: 10.1126/scitranslmed.abq5753] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Genetic variants among individuals have been associated with ineffective control of hypertension. Previous work has shown that hypertension has a polygenic nature, and interactions between these loci have been associated with variations in drug response. Rapid detection of multiple genetic loci with high sensitivity and specificity is needed for the effective implementation of personalized medicine for the treatment of hypertension. Here, we used a cationic conjugated polymer (CCP)-based multistep fluorescence resonance energy transfer (MS-FRET) technique to qualitatively analyze DNA genotypes associated with hypertension in the Chinese population. Assessment of 10 genetic loci using this technique successfully identified known hypertensive risk alleles in a retrospective study of whole-blood samples from 150 patients hospitalized with hypertension. We then applied our detection method in a prospective clinical trial of 100 patients with essential hypertension and found that personalized treatment of patients with hypertension based on results from the MS-FRET technique could effectively improve blood pressure control rate (94.0% versus 54.0%) and shorten the time duration to controlling blood pressure (4.06 ± 2.10 versus 5.82 ± 1.84 days) as compared with conventional treatment. These results suggest that CCP-based MS-FRET genetic variant detection may assist clinicians in rapid and accurate classification of risk in patients with hypertension and improve treatment outcomes.
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Affiliation(s)
- Qi Shen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Honghong Zhang
- Cardiac Department, Sixth Center of Chinese PLA General Hospital; Cardiac Department, First Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases; Department of Cardiology & National Clinical Research Center of Geriatric Disease; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, First Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Yiming Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Mingyu Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hao Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Zhiwen Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Haijing Zhao
- Cardiac Department, Sixth Center of Chinese PLA General Hospital; Cardiac Department, First Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases; Department of Cardiology & National Clinical Research Center of Geriatric Disease; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, First Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Qi Liu
- Cardiac Department, Sixth Center of Chinese PLA General Hospital; Cardiac Department, First Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases; Department of Cardiology & National Clinical Research Center of Geriatric Disease; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, First Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Zihao Fu
- Cardiac Department, Sixth Center of Chinese PLA General Hospital; Cardiac Department, First Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases; Department of Cardiology & National Clinical Research Center of Geriatric Disease; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, First Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Yufei Di
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Haotian Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yundai Chen
- Cardiac Department, Sixth Center of Chinese PLA General Hospital; Cardiac Department, First Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases; Department of Cardiology & National Clinical Research Center of Geriatric Disease; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, First Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Yuqi Liu
- Cardiac Department, Sixth Center of Chinese PLA General Hospital; Cardiac Department, First Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases; Department of Cardiology & National Clinical Research Center of Geriatric Disease; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, First Center of Chinese PLA General Hospital, Beijing 100141, P.R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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5
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Megha, Kumar V, Kaur P, Singh K. Julolidine-hydrazone based chemosensor for detection of Zn 2+: Fluorescent in-situ formed Zn 2+ complex discriminates PPi from ADP and ATP. Anal Chim Acta 2023; 1240:340758. [PMID: 36641143 DOI: 10.1016/j.aca.2022.340758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
In the present investigation, we have designed and synthesised Zn2+ sensitive Julolidine-hydrazone (JSB) based chemosensor, which crystallised in a monoclinic crystal system with P21/c space group. The bare JSB was nonemissive, but in the presence of Zn2+ ions in solution it showed emission, ascribed to the chelation enhanced emission process, which is also utilised to detect Zn2+ in water samples. Comparing the chromaticity coordinates deduced from the emission colors of the JSB-Zn2+ in solution, powder and hybrid polymer thin film, using CIE (Commission Internationale de I'Eclairage 1931) chromaticity diagram, it was found that compared to the emission of the solution, the emission of the powder was red shifted, while that of the thin film was blue shifted. Further, the sensing of Zn2+ showed reversibility in the presence of pyrophosphate (PPi), which allowed quantification of PPi. Interestingly, in addition to the detection of PPi using the in-situ formed JSB-Zn2+ complex, the process was selective and discriminated PPi from ADP and ATP. The detection of PPi was rationalized via a decomplexation reaction, and translated in the construction of INHIBIT logic gate. Additionally, the possible use of the JSB coated sensor paper for the on-site detection of Zn2+ and subsequent JSB-Zn2+ complex for PPi ions has been demonstrated. The experimental results showed good correlation with the theoretical calculations wherever possible.
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Affiliation(s)
- Megha
- Department of Chemistry, Centre of Advanced Study, Guru Nanak Dev University, Amritsar, 143005, India
| | - Virendra Kumar
- Department of Chemistry, Centre of Advanced Study, Guru Nanak Dev University, Amritsar, 143005, India
| | - Paramjit Kaur
- Department of Chemistry, Centre of Advanced Study, Guru Nanak Dev University, Amritsar, 143005, India.
| | - Kamaljit Singh
- Department of Chemistry, Centre of Advanced Study, Guru Nanak Dev University, Amritsar, 143005, India.
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6
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Park DH, Choi MY, Choi JH. Recent Development in Plasmonic Nanobiosensors for Viral DNA/RNA Biomarkers. BIOSENSORS 2022; 12:bios12121121. [PMID: 36551088 PMCID: PMC9776357 DOI: 10.3390/bios12121121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 05/28/2023]
Abstract
Recently, due to the coronavirus pandemic, the need for early diagnosis of infectious diseases, including viruses, is emerging. Though early diagnosis is essential to prevent infection and progression to severe illness, there are few technologies that accurately measure low concentrations of biomarkers. Plasmonic nanomaterials are attracting materials that can effectively amplify various signals, including fluorescence, Raman, and other optical and electromagnetic output. In this review, we introduce recently developed plasmonic nanobiosensors for measuring viral DNA/RNA as potential biomarkers of viral diseases. In addition, we discuss the future perspective of plasmonic nanobiosensors for DNA/RNA detection. This review is expected to help the early diagnosis and pathological interpretation of viruses and other diseases.
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7
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Mukherjee P, Chatterjee S, Mukherjee S, Das D. Dual Responsive Optical Sensor for The Detection of Zn
2+
and Al
3+
: Supportive Single‐Crystal X‐ray Structure of its Ni(II) Complex and DFT Studies. ChemistrySelect 2022. [DOI: 10.1002/slct.202203179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Pallabi Mukherjee
- Department of Chemistry The University of Burdwan Burdwan 713104, W.B. India
| | - Sudeshna Chatterjee
- Department of Chemistry The University of Burdwan Burdwan 713104, W.B. India
| | - Sukriti Mukherjee
- Department of Chemistry The University of Burdwan Burdwan 713104, W.B. India
| | - Debasis Das
- Department of Chemistry The University of Burdwan Burdwan 713104, W.B. India
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8
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Adampourezare M, Hasanzadeh M, Seidi F. Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects. RSC Adv 2022; 12:25786-25806. [PMID: 36199327 PMCID: PMC9460980 DOI: 10.1039/d2ra03630d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/03/2022] [Indexed: 12/02/2022] Open
Abstract
DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed. Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.![]()
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Affiliation(s)
- Mina Adampourezare
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
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9
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Zhao L, Zhao C, Zhou J, Ji H, Qin Y, Li G, Wu L, Zhou X. Conjugated Polymers-based Luminescent Probes for Ratiometric Detection of Biomolecules. J Mater Chem B 2022; 10:7309-7327. [DOI: 10.1039/d2tb00937d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate monitoring of the biomolecular changes in biological and physiological environments is of great significance for pathogenesis, development, diagnosis and treatment of diseases. Compared with traditional luminescent probes on the...
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10
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Ghorui T, Hens A, Pramanik K. Synthesis, photophysical properties and theoretical studies of pyrrole-based azoaromatic Zn(II) complexes in mixed aqueous medium. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Choi JH, Ha T, Shin M, Lee SN, Choi JW. Nanomaterial-Based Fluorescence Resonance Energy Transfer (FRET) and Metal-Enhanced Fluorescence (MEF) to Detect Nucleic Acid in Cancer Diagnosis. Biomedicines 2021; 9:928. [PMID: 34440132 PMCID: PMC8392676 DOI: 10.3390/biomedicines9080928] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
Nucleic acids, including DNA and RNA, have received prodigious attention as potential biomarkers for precise and early diagnosis of cancers. However, due to their small quantity and instability in body fluids, precise and sensitive detection is highly important. Taking advantage of the ease-to-functionality and plasmonic effect of nanomaterials, fluorescence resonance energy transfer (FRET) and metal-enhanced fluorescence (MEF)-based biosensors have been developed for accurate and sensitive quantitation of cancer-related nucleic acids. This review summarizes the recent strategies and advances in recently developed nanomaterial-based FRET and MEF for biosensors for the detection of nucleic acids in cancer diagnosis. Challenges and opportunities in this field are also discussed. We anticipate that the FRET and MEF-based biosensors discussed in this review will provide valuable information for the sensitive detection of nucleic acids and early diagnosis of cancers.
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Affiliation(s)
- Jin-Ha Choi
- School of Chemical Engineering, Jeonbuk National University, Jeonju 54896, Korea;
| | - Taehyeong Ha
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Korea; (T.H.); (M.S.)
| | - Minkyu Shin
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Korea; (T.H.); (M.S.)
| | - Sang-Nam Lee
- Uniance Gene Inc., 1107 Teilhard Hall, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Korea
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Korea; (T.H.); (M.S.)
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12
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Liu X, Peng X, Xu F, Wang L, Liu M. Highly Selective Schiff-Base Fluorescent Probe for Rare Earth Ion Lu3+. RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363221060165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Shao Y, Kong J, Xu H, Wu X, Cao Y, Li W, Han J, Li D, Xie K, Wu J. OPCML Methylation and the Risk of Ovarian Cancer: A Meta and Bioinformatics Analysis. Front Cell Dev Biol 2021; 9:570898. [PMID: 33777925 PMCID: PMC7990783 DOI: 10.3389/fcell.2021.570898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The association of opioid binding protein cell adhesion molecule-like (OPCML) gene methylation with ovarian cancer risk remains unclear. Methods: We identified eligible studies by searching the PubMed, Web of Science, ScienceDirect, and Wanfang databases. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were used to determine the association of OPCML methylation with ovarian cancer risk. Meta-regression and subgroup analysis were used to assess the sources of heterogeneity. Additionally, we analyzed the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets to validate our findings. Results: Our study included 476 ovarian cancer patients and 385 controls from eight eligible studies. The pooled OR was 33.47 (95% CI = 12.43-90.16) in the cancer group vs. the control group under the random-effects model. The association was still significant in subgroups according to sample type, control type, methods, and sample sizes (all P < 0.05). Sensitivity analysis showed that the finding was robust. No publication bias was observed in Begg's (P = 0.458) and Egger's tests (P = 0.261). We further found that OPCML methylation was related to III/IV (OR = 4.20, 95% CI = 1.59-11.14) and poorly differentiated grade (OR = 4.37; 95% CI = 1.14-16.78). Based on GSE146552 and GSE155760, we validated that three CpG sites (cg16639665, cg23236270, cg15964611) in OPCML promoter region were significantly higher in cancer tissues compared to normal tissues. However, we did not observe the associations of OPCML methylation with clinicopathological parameters and overall survival based on TCGA ovarian cancer data. Conclusion: Our findings support that OPCML methylation is associated with an increased risk of ovarian cancer.
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Affiliation(s)
- Yang Shao
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China.,The First People's Hospital of Zhangjiagang City, The Zhangjiagang Affiliated Hospital of Soochow University, Suzhou, China
| | - Jing Kong
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Hanzi Xu
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoli Wu
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - YuePeng Cao
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Weijian Li
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Han
- Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dake Li
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Kaipeng Xie
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiangping Wu
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
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14
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Araiza-Olivera D, Gutierrez-Aguilar M, Espinosa-García AM, García-García JA, Tapia-Orozco N, Sánchez-Pérez C, Palacios-Reyes C, Escárcega D, Villalón-López DN, García-Arrazola R. From bench to bedside: Biosensing strategies to evaluate endocrine disrupting compounds based on epigenetic events and their potential use in medicine. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 80:103450. [PMID: 32622887 DOI: 10.1016/j.etap.2020.103450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The relationship between endocrine system disorders and health risks due to chemical environmental compounds has become a growing concern in recent years. Involuntary exposure to endocrine disruptors (EDCs) is associated with the worldwide increase of diseases such as cancer, obesity, diabetes, and neurocortical disorders. EDCs are compounds that target the nuclear hormonereceptors (NHR) leading to epigenetic changes. Consequently, the use of biosensing strategies based on epigenetic events have a great potential to provide outstanding information about the exposition of EDCs and their evaluation in human health. This review addresses the novel trends in biosensing EDCs evaluation based on DNA methylation assays associated with different human diseases.
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Affiliation(s)
- D Araiza-Olivera
- Department of Chemistry and Biomolecules, Institute of Chemistry, UNAM, Mexico.
| | | | - A M Espinosa-García
- Unidad de Medicina Genómica, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - J A García-García
- Department of Education, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - N Tapia-Orozco
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Sánchez-Pérez
- Institute of Applied Sciences and Technology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Palacios-Reyes
- Laboratory of Genetics and Molecular Diagnostics, Juarez Hospital of Mexico, Mexico City, Mexico.
| | - D Escárcega
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Ciudad de México, calle del Puente 222, Ejidos de Huipulco, Tlalpan 14380, Mexico City, Mexico.
| | - Demelza N Villalón-López
- Instituto Politénico Nacional-Escuela Nacional de Ciencias Biológicas, Departamento de Química Orgánica, Prolongación de Carpio y Plande Ayala, colonia Casco de Santo Tomás. Del, Miguel Hidalgo, 11350, Mexico.
| | - R García-Arrazola
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
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15
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Zhang Y, Li CC, Zhang X, Xu Q, Zhang CY. Development of Oxidation Damage Base-Based Fluorescent Probe for Direct Detection of DNA Methylation. Anal Chem 2020; 92:10223-10227. [PMID: 32664718 DOI: 10.1021/acs.analchem.0c01880] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation has become a promising epigenetic biomarker for cancer diagnosis, prognosis, and therapy monitoring. Herein, we demonstrate for the first time the development of a new oxidation damage base (8-oxo-7,8-dihydroguanine (8-oxoG))-modified fluorescent probe for direct detection of DNA methylation. This fluorescent probe is labeled with carboxy-X-rhodamine (ROX) and black hole quencher 2 (BHQ2) at the 5' and 3' termini, respectively, with one 8-oxoG base modification in the middle position, and it can discriminate the methylated cytosine from the unmethylated cytosine. The presence of target methylated DNA may induce the recycle cleavage of fluorescent probes with the assistance of human 8-oxoG DNA glycosylase 1 (hOGG1) enzyme, resulting in an enhanced fluorescence signal. In comparison with the reported bisulfite treatment-based indirect approaches, this fluorescent probe can be used for direct detection of DNA methylation under isothermal conditions without the requirement of a stringent primer/template design, any thermal cycling, and ligation procedures, greatly simplifying the experimental processes. Moreover, this fluorescent probe exhibits good specificity and high sensitivity, and it can distinguish a 0.01% methylation level even in the presence of excess unmethylated DNA. Furthermore, this fluorescent probe can be used to detect DNA methylation in genomic DNA extracted from human colon cancer cells, holding great potential in epigenetic study and early clinical diagnosis.
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Affiliation(s)
- Yan 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, Shandong 250014, China
| | - Chen-Chen Li
- 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, Shandong 250014, China
| | - Xuechong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. 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, Shandong 250014, China
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16
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Dey S, Purkait R, Mallick D, Sinha C. A Vanillinyl‐Hydrazone Schiff Base: Recognition of Mg
2+
, Zn
2+
, Cd
2+
and I
−
by Turn‐On Fluorescence Method. ChemistrySelect 2020. [DOI: 10.1002/slct.202002271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sunanda Dey
- Department of Chemistry Jadavpur University Kolkata 700 032 India
| | - Rakesh Purkait
- Department of Chemistry Jadavpur University Kolkata 700 032 India
| | - Debashis Mallick
- Department of Chemistry Mrinalini Datta Mahavidyapith Kolkata 700 051 India
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17
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Ma L, Huang Y, Zhang H, Ning W, Qi R, Yuan H, Lv F, Liu L, Yu C, Wang S. Sensitive Detection and Conjoint Analysis of Promoter Methylation by Conjugated Polymers for Differential Diagnosis and Prognosis of Glioma. ACS APPLIED MATERIALS & INTERFACES 2020; 13:9291-9299. [PMID: 32436715 DOI: 10.1021/acsami.0c03218] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glioma is the most common primary tumor in the central nervous system (CNS) with the worst prognosis. Accurate pathological diagnosis has always been a challenge for optimal management of glioma. Promoter methylation is an important mechanism of epigenetic silencing tumor-suppressor genes and a potential biomarker for differential diagnosis and prognosis. Herein, using the cationic conjugated polymer (CCP)-based fluorescence resonance energy transfer (FRET) technique, we realized a highly sensitive detection of promoter methylation in clinical samples of minimal methylation degree (1.25%) and trace DNA quantity (10 ng/μL). Results for three glioma-related genes (MGMT, CDKN2A, and TERT) were combined in a diagnostic classifier to analyze the glioma-CpG island methylator phenotype (G-CIMP), which achieved a sensitivity of 80% at a maximum specificity of 100% for a glioma diagnosis. Kaplan-Meier survival curves and Pearson correlation analysis revealed that the prognosis of glioma patients with high G-CIMP scores (>5) was significantly better than those with low G-CIMP scores, especially in diffuse midline glioma and astrocytoma. This CCP-based FRET technique for determining G-CIMP status could provide patients with rapid and reasonably accurate diagnosis of glioma, as well as a valuable prognostic prediction that can guide individual treatment.
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Affiliation(s)
- Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Yiming Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Ruilian Qi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Haitao Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Chunjiang Yu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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18
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Zhang P, Qiu T, Liu L, Lv F, Li Z, Ying J, Wang S. Conjoint Analysis of DNA Methylation for Tumor Differentiation Using Cationic Conjugated Polymers. ACS APPLIED BIO MATERIALS 2020; 3:2867-2872. [PMID: 35025334 DOI: 10.1021/acsabm.0c00047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Molecular biomarkers, especially DNA methylation, are crucial discoveries for early detection of cancer. Compared with a single biomarker detection mode, using the conjoint detection mode can allow researchers to easily assess the association of the biomarkers with specific cancer. In this paper, we calculated the methylation status of RASSF1A, APC, CDKN2A/p16, and TMEFF2 genes using cationic conjugated polymers (CCPs)-based fluorescence resonance energy transfer (FRET) technique and then explored the connection between the overall DNA methylation status of the four genes and the clinical parameters of lung cancer patients. After analysis, no association was found between the methylation status of any single gene and the grade of tumor differentiation among 159 lung cancer samples analyzed. However, for conjoint analysis using the four genes, a statistically significant difference was reached between methylation status and the grade of tumor differentiation. The methylation levels in a panel of the four genes were correlated with sex, age, smoking pack-years, and lymphatic metastasis. Therefore, the conjoint analysis of DNA methylation in specific cancer-related genes could be a useful diagnostic tool for clinical implementation.
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Affiliation(s)
- Pengbo Zhang
- School of Chemistry and Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P. R. China.,Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Tian Qiu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P. R. China
| | - Libing Liu
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fengting Lv
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P. R. China
| | - Shu Wang
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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19
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Dong X, Zheng T, Zhang Z, Bai X, Li H, Zhang J. [Luteolin reverses OPCML methylation to inhibit proliferation of breast cancer MDA-MB-231 cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:550-555. [PMID: 32895125 DOI: 10.12122/j.issn.1673-4254.2020.04.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To observe the effect of luteolin on the proliferation and expression of OPCML in breast cancer cell line MDA-MB-231. METHODS Cultured MDA-MB-231 cells were treated with luteolin at the concentrations of 5, 10 and 20 μmol/L for 24 or 48 h. MTT assay was used to detect cell proliferation and flow cytometry was used to detect the cell apoptosis. The expressions of OPCML mRNA and protein were detected using real-time quantitative PCR and Western blotting, respectively. OPCML gene methylation in the promoter region was detected using methylation-specific PCR (MSP), and the activity of methylase in the cells was analyzed. RESULTS MTT assay showed that treatment with luteolin at 5, 10 and 20 μmol/L for 24 h concentration-dependently decreased the viability of MDA-MB-231 cells (P < 0.05). Flow cytometry also showed that luteolin at different concentrations could induce apoptosis of MDA-MB-231 cells (P < 0.05). Luteolin dose-dependently induced the expression of OPCML mRNA and protein in MDA-MB-231 cells (P < 0.05), down-regulated the methylation status in the promoter region of OPCML gene, up-regulated the level of non-methylated OPCML, and reduced the activity of methylase in the cells (P < 0.05). CONCLUSIONS Luteolin inhibits the proliferation of MDA-MB-231 breast cancer cells probably by upregulating OPCML expression and its demethylation.
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Affiliation(s)
- Xinmin Dong
- Department of Oncology, Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Ti Zheng
- Medical Departmentn, Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Ziying Zhang
- Department of Basic Medicine, School of Pharmacology of Inner Mongolia Medical University, Hohhot 010110, China
| | - Xiling Bai
- Department of Interventional Riadiology, Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot 010010, China
| | - Hua Li
- Department of Oncology, Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Jian Zhang
- Department of Radiotherapy, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
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20
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Fu J, Li B, Mei H, Chang Y, Xu K. Fluorescent schiff base probes for sequential detection of Al 3+ and F - and cell imaging applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117678. [PMID: 31676151 DOI: 10.1016/j.saa.2019.117678] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 09/28/2019] [Accepted: 10/17/2019] [Indexed: 05/06/2023]
Abstract
Two novel Schiff-base fluorescent probers SQ and NQ based on 8-hydroxyquinoline moiety were designed and synthesized. The both probes were capable of binding with Al3+ by naked eye detection to produce a significant fluorescence enhancement response with a detection limit of 1.48 × 10-8 and 4.23 × 10-8 M, respectively. At the same time, the formed complexes SQ-Al3+ and NQ-Al3+ could sequentially detect F-, and the detection limits of F- were determined to be 1.64 × 10-7 and 3.58 × 10-8 M, respectively. The "off-on-off" fluorescence response process demonstrated that the binding were reversible. The probes were further successfully utilized to detect Al3+ and F- in vitro PC12 cells.
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Affiliation(s)
- Jiaxin Fu
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China
| | - Bai Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China
| | - Huihui Mei
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China
| | - Yongxin Chang
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China
| | - Kuoxi Xu
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China.
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21
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Advances in oligonucleotide-based detection coupled with fluorescence resonance energy transfer. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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22
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Asaithambi G, Periasamy V, Karuppannan N. Fluorescence sensing response of zinc(II) and pyrophosphate ions by benzoxazole appended dipodal Schiff base. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2018.10.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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23
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Anantha-Iyengar G, Shanmugasundaram K, Nallal M, Lee KP, Whitcombe MJ, Lakshmi D, Sai-Anand G. Functionalized conjugated polymers for sensing and molecular imprinting applications. Prog Polym Sci 2019. [DOI: 10.1016/j.progpolymsci.2018.08.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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24
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Leng X, Xu W, Qiao C, Jia X, Long Y, Yang B. New rhodamine B-based chromo-fluorogenic probes for highly selective detection of aluminium(iii) ions and their application in living cell imaging. RSC Adv 2019; 9:6027-6034. [PMID: 35517253 PMCID: PMC9060861 DOI: 10.1039/c8ra09850f] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/03/2019] [Indexed: 11/24/2022] Open
Abstract
Two rhodamine B-based fluorescent probes, BOS1 and BOS2, were designed and synthesized with good yields via the condensation reactions between the o-diaminobenzene modified rhodamine core structure (RBO) and salicylaldehyde derivatives. Both the probes exhibited remarkable absorbance-on and fluorescence-on responses to Al3+ over other metal ions in ethanol–water (1 : 9, v/v) medium via the rhodamine ring-opening approach, which can be used for “naked-eye” Al3+ detection over a broad pH range (5–9). The fluorescence intensities of the probes were linear with the Al3+ ion concentration, resulting in a low limit of detection of 1.839 μM (BOS1) and 1.374 μM (BOS2) for Al3+. In addition, the MTT assays and cell imaging experiments of Al3+ in SGC-7901 living cells demonstrated that the probes had negligible cytotoxicity, and were cell permeable and suitable for sensing Al3+ in biological systems. Two rhodamine B-based fluorescent probes exhibited remarkable absorbance-on and fluorescence-on responses to Al3+, which can be used for biological imaging.![]()
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Affiliation(s)
- Xin Leng
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710127
- China
| | - Wenfeng Xu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710127
- China
| | - Chengfang Qiao
- Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources
- College of Chemical Engineering and Modern Materials
- Shangluo University
- Shangluo 726000
- China
| | - Xu Jia
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710127
- China
| | - Ying Long
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710127
- China
| | - Bingqin Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710127
- China
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25
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Syedmoradi L, Esmaeili F, Norton ML. Towards DNA methylation detection using biosensors. Analyst 2018; 141:5922-5943. [PMID: 27704092 DOI: 10.1039/c6an01649a] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation, a stable and heritable covalent modification which mostly occurs in the context of a CpG dinucleotide, has great potential as a biomarker to detect disease, provide prognoses and predict therapeutic responses. It can be detected in a quantitative manner by many different approaches both genome-wide and at specific gene loci, in various biological fluids such as urine, plasma, and serum, which can be obtained without invasive procedures. The current, classical methods are effective in studying DNA methylation patterns, however, for the most part; they have major drawbacks such as expensive instruments, complicated and time consuming protocols as well as relatively low sensitivity, and high false positive rates. To overcome these obstacles, great efforts have been made toward the development of reliable sensor devices to solve these limitations, providing sensitive, fast and cost-effective measurements. The use of biosensors for DNA methylation biomarkers has increased in recent years, because they are portable, simple, rapid, and inexpensive which offers a straightforward way to detect methylated biomarkers. In this review, we give an overview of the conventional techniques for the detection of DNA methylation and then will focus on recent advances in biosensor based methylation detection that eliminate bisulfite conversion and PCR amplification.
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Affiliation(s)
- Leila Syedmoradi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Esmaeili
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael L Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, WV 25755, USA.
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Simultaneous biosensing of CA125 and CA15-3 tumor markers and imaging of OVCAR-3 and MCF-7 cells lines via bi-color FRET phenomenon using dual blue-green luminescent carbon dots with single excitation wavelength. Int J Biol Macromol 2018; 118:617-628. [DOI: 10.1016/j.ijbiomac.2018.06.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 01/11/2023]
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27
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Singh R, Samanta S, Mullick P, Ramesh A, Das G. Al3+ sensing through different turn-on emission signals vis-à-vis two different excitations: Applications in biological and environmental realms. Anal Chim Acta 2018; 1025:172-180. [DOI: 10.1016/j.aca.2018.03.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 10/17/2022]
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28
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Lu X, Jia H, Yan X, Wang J, Wang Y, Liu C. Label-free detection of histone based on cationic conjugated polymer-mediated fluorescence resonance energy transfer. Talanta 2018; 180:150-155. [DOI: 10.1016/j.talanta.2017.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/28/2017] [Accepted: 12/02/2017] [Indexed: 12/30/2022]
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29
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Commercial glucometer as signal transducer for simple evaluation of DNA methyltransferase activity and inhibitors screening. Anal Chim Acta 2018; 1001:18-23. [DOI: 10.1016/j.aca.2017.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/31/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
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30
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Cui WR, Li ZJ, Chi BZ, Li ZM, Liang RP, Qiu JD. Ultrasensitively electrochemical detection activity of DNA methyltransferase using an autocatalytic and recycling amplification strategy. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2017.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Wang J, Lv F, Liu L, Ma Y, Wang S. Strategies to design conjugated polymer based materials for biological sensing and imaging. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2017.06.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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32
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Guo L, Hu Y, Zhang Z, Tang Y. Universal fluorometric aptasensor platform based on water-soluble conjugated polymers/graphene oxide. Anal Bioanal Chem 2017; 410:287-295. [DOI: 10.1007/s00216-017-0720-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/18/2022]
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33
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Rezk NA, Mohamed RH, Alnemr AA, Harira M. Promoter Methylation of RASSF1A Gene in Egyptian Patients with Ovarian Cancer. Appl Biochem Biotechnol 2017; 185:153-162. [PMID: 29098560 DOI: 10.1007/s12010-017-2648-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/26/2017] [Indexed: 12/14/2022]
Abstract
Ovarian malignancy is diagnosed in nearly a fourth of a million women internationally every year. Methylation of RASSF1A tumor suppressor gene prompts its inactivation in diseases. In this study, the RASSF1A promoter methylation was detected by methylated-specific PCR and investigated serum RASSF1A protein level through enzyme-linked immunosorbant assay in 160 Egyptian patients with ovarian cancer and 160 healthy controls. The present work proved that there was a higher frequency of RASSF1A methylation and a decrease in its serum level in patients with ovarian cancer compared to controls as well as in the high-grade tumor patients compared to low grade ones and also in advanced ovarian tumor stage compared to early stages. Our study exhibited that RASSF1A promoter hypermethylation and its protein levels may be a reliable and sensitive tool for diagnosing and monitoring of ovarian malignancy patients.
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Affiliation(s)
- Noha A Rezk
- Medical Biochemistry Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt.
| | - Rasha H Mohamed
- Biochemistry Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Amr AbdAlmohsen Alnemr
- Obstetrics and Gynecology Departments, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Mervat Harira
- Obstetrics and Gynecology Departments, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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Hosseini M, Khaki F, Shokri E, Khabbaz H, Dadmehr M, Ganjali MR, Feizabadi M, Ajloo D. Study on the Interaction of the CpG Alternating DNA with CdTe Quantum Dots. J Fluoresc 2017; 27:2059-2068. [PMID: 28842837 DOI: 10.1007/s10895-017-2145-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/18/2017] [Indexed: 12/31/2022]
Abstract
A novel sensitive method for detection of DNA methylation was developed with thioglycollic acid (TGA)-capped CdTe quantum dots (QDs) as fluorescence probes. Recognition of methylated DNA sites would be useful strategy due to the important roles of methylation in disease occurrence and developmental processes. DNA methylation occurs most often at cytosine-guanine sites (CpG dinucleotides) of gene promoters. The QDs significantly interacted with hybridized unmethylated and methylated DNA. The interaction of CpG rich methylated and unmethylated DNA hybrid with quantum dots as an optical probe has been investigated by fluorescence spectroscopy and electrophoresis assay. The fluorescence intensity of QDs was highly dependent to unmethylated and methylated DNA. Specific site of CpG islands of Adenomatous polyposis coli (APC), a well-studied tumor suppressor gene, was used as the detection target. Under optimum conditions, upon the addition of unmethylated dsDNA, the fluorescence intensity increased in linear range from 1.0 × 10- 10 to 1.0 × 10- 6M with detection limit of 6.2 × 10- 11 M and on the other hand, the intensity of QDs showed no changes with addition of methylated dsDNA. We also demonstrated that the unmethylated and methylated DNA and QDs complexes showed different mobility in electrophoresis assay. This easy and reliable method could distinguish between methylated and unmethylated DNA sequences.
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Affiliation(s)
- Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Freshteh Khaki
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Ehsan Shokri
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Hossein Khabbaz
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mehdi Dadmehr
- Department of Biotechnology, Payame Noor University, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran.,Biosensor Research Center, Endocrinology & Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Davood Ajloo
- School of Chemistry, Damghan University, Damghan, Iran
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Du C, Hu Y, Zhang Q, Guo Z, Ge G, Wang S, Zhai C, Zhu M. Competition-derived FRET-switching cationic conjugated polymer-Ir(III) complex probe for thrombin detection. Biosens Bioelectron 2017; 100:132-138. [PMID: 28886457 DOI: 10.1016/j.bios.2017.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 07/14/2017] [Accepted: 08/07/2017] [Indexed: 02/04/2023]
Abstract
A novel, label-free and convenient strategy for thrombin assay has been developed based on the fluorescence resonance energy transfer (FRET) from a cationic conjugated polymer (CCP) to Ir(III) complex. The energy donor (CCP) and acceptor (Ir(III) complex) were taken into close proximity through π-π stacking interaction and electrostatic interaction, leading to the occurrence of FRET. However, the introduction of the thrombin aptamer upset the status and blocked the FRET process, but afterwards the reappearance of FRET phenomenon was confirmed by the special binding interaction between aptamer and thrombin, thus achieving the quantitative detection of thrombin. This assay could detect thrombin as low concentration as about 0.05pM and provided a highly specific selectivity among other nonspecific proteins. Moreover, the strategy may allow our platform to provide similar sensitivity toward different targets in an aptamer-structure-independent manner. Furthermore, the assay can be used to detect thrombin in diluted real urine or serum samples with a satisfactory recovery, implying its great potential for rapid detection of thrombin in the clinic.
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Affiliation(s)
- Chunnuan Du
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Yufang Hu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China.
| | - Qingqing Zhang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Zhiyong Guo
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Guoping Ge
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China.
| | - Sui Wang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Chunyang Zhai
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Mingshan Zhu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
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36
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Kulkarni B, Jayakannan M. Fluorescent-Tagged Biodegradable Polycaprolactone Block Copolymer FRET Probe for Intracellular Bioimaging in Cancer Cells. ACS Biomater Sci Eng 2017; 3:2185-2197. [DOI: 10.1021/acsbiomaterials.7b00426] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bhagyashree Kulkarni
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Manickam Jayakannan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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37
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Swift T, Paul N, Swanson L, Katsikogianni M, Rimmer S. Förster Resonance Energy Transfer across interpolymer complexes of poly(acrylic acid) and poly(acrylamide). POLYMER 2017. [DOI: 10.1016/j.polymer.2017.06.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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38
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Gao F, Fan T, Ou S, Wu J, Zhang X, Luo J, Li N, Yao Y, Mou Y, Liao X, Geng D. Highly efficient electrochemical sensing platform for sensitive detection DNA methylation, and methyltransferase activity based on Ag NPs decorated carbon nanocubes. Biosens Bioelectron 2017; 99:201-208. [PMID: 28759870 DOI: 10.1016/j.bios.2017.07.063] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022]
Abstract
In this paper, we reported a sensitive and selective electrochemical method for quantify DNA methylation, analyzing DNA MTase activity and screening of MTase inhibitor based on silver nanoparticles (Ag NPs) decorated carbon nanocubes (CNCs) as signal tag. The Ag NPs/CNCs was prepared by in situ growth of nanosilver on carboxylated CNCs and used as a tracing tag to label antibody. The sensor was prepared by immobilizing the double DNA helix structure on the surface of gold electrode. When DNA MTase was introduced, the probe was methylated. Successively, anti-5-methylcytosine antibody labeled Ag NPs/CNCs was specifically conjugated on the CpG methylation site. The electrochemical stripping signal of the Ag NPs was used to monitor the activity of MTase. The electrochemical signal has a linear relationship with M.SssI activities ranging from 0.05 to 120U/mL with a detection limit of 0.03U/mL. In addition, we also demonstrated the method could be used for rapid evaluation and screening of the inhibitors of MTase. The newly designed strategy avoid the requirement of deoxygenation for electrochemical assay, and thus provide a promising potential in clinical application.
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Affiliation(s)
- Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China; Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Taotao Fan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Shanshan Ou
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Jing Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Xing Zhang
- The Graduate School, Xuzhou Medical University, 221004 Xuzhou, China
| | - Jianjun Luo
- The Graduate School, Xuzhou Medical University, 221004 Xuzhou, China
| | - Na Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Yao Yao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Yingfeng Mou
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Xianjiu Liao
- School of Pharmacy, Youjiang Medical University for Nationalities, 533000 Baise, China.
| | - Deqin Geng
- The Graduate School, Xuzhou Medical University, 221004 Xuzhou, China; Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China.
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39
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Zhang X, Zhao Q, Li Y, Duan X, Tang Y. Multifunctional Probe Based on Cationic Conjugated Polymers for Nitroreductase-Related Analysis: Sensing, Hypoxia Diagnosis, and Imaging. Anal Chem 2017; 89:5503-5510. [DOI: 10.1021/acs.analchem.7b00477] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Xiaoqian Zhang
- Key Laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, Key Laboratory of
Applied Surface and Colloid Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710062, P. R. China
| | - Qi Zhao
- Key Laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, Key Laboratory of
Applied Surface and Colloid Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710062, P. R. China
| | - Yanru Li
- Key Laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, Key Laboratory of
Applied Surface and Colloid Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710062, P. R. China
| | - Xinrui Duan
- Key Laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, Key Laboratory of
Applied Surface and Colloid Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710062, P. R. China
| | - Yanli Tang
- Key Laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, Key Laboratory of
Applied Surface and Colloid Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710062, P. R. China
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40
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Haque MH, Gopalan V, Islam MN, Masud MK, Bhattacharjee R, Hossain MSA, Nguyen NT, Lam AK, Shiddiky MJA. Quantification of gene-specific DNA methylation in oesophageal cancer via electrochemistry. Anal Chim Acta 2017; 976:84-93. [PMID: 28576321 DOI: 10.1016/j.aca.2017.04.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023]
Abstract
Development of simple and inexpensive method for the analysis of gene-specific DNA methylation is important for the diagnosis and prognosis of patients with cancer. Herein, we report a relatively simple and inexpensive electrochemical method for the sensitive and selective detection of gene-specific DNA methylation in oesophageal cancer. The underlying principle of the method relies on the affinity interaction between DNA bases and unmodified gold electrode. Since the affinity trend of DNA bases towards the gold surface follows as adenine (A) > cytosine (C) > guanine (G)> thymine (T), a relatively larger amount of bisulfite-treated adenine-enriched unmethylated DNA adsorbs on the screen-printed gold electrodes (SPE-Au) in comparison to the guanine-enriched methylated sample. The methylation levels were (i.e., different level of surface attached DNA molecules due to the base dependent differential adsorption pattern) quantified by measuring saturated amount of charge-compensating [Ru(NH3)6]3+ molecules in the surface-attached DNAs by chronocoulometry as redox charge of the [Ru(NH3)6]3+ molecules quantitatively reflects the amount of the adsorbed DNA confined at the electrode surface. The assay could successfully distinguish methylated and unmethylated DNA sequences at single CpG resolution and as low as 10% differences in DNA methylation. In addition, the assay showed fairly good reproducibility (% RSD= <5%) with better sensitivity and specificity by analysing various levels of methylation in two cell lines and eight fresh tissues samples from patients with oesophageal squamous cell carcinoma. Finally, the method was validated with methylation specific-high resolution melting curve analysis and Sanger sequencing methods.
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Affiliation(s)
- Md Hakimul Haque
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia; School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia.
| | - Md Nazmul Islam
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Mostafa Kamal Masud
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials, University of Wollongong, NSW 2519, Australia
| | - Ripon Bhattacharjee
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Md Shahriar Al Hossain
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials, University of Wollongong, NSW 2519, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia.
| | - Muhammad J A Shiddiky
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
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41
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Chowdhury B, Cho IH, Irudayaraj J. Technical advances in global DNA methylation analysis in human cancers. J Biol Eng 2017; 11:10. [PMID: 28261325 PMCID: PMC5331624 DOI: 10.1186/s13036-017-0052-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/10/2017] [Indexed: 02/07/2023] Open
Abstract
Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-methylcytosine (5mC) patterns, commonly observed during tumorigenesis, give rise to misregulated biological pathways beneficial to the rapidly propagating tumor mass but deleterious to the healthy tissues of the affected individual. A growing body of evidence suggests that the global DNA methylation levels could serve as utilitarian biomarkers in certain cancer types. Important breakthroughs in the recent years have uncovered further oxidized derivatives of 5mC - 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), thereby expanding our understanding of the DNA methylation dynamics. While the biological roles of these epigenetic derivatives are being extensively characterized, this review presents a perspective on the opportunity of innovation in the global methylation analysis platforms. While multiple methods for global analysis of 5mC in clinical samples exist and have been reviewed elsewhere, two of the established methods - Liquid Chromatography coupled with mass spectrometry (LC-MS/MS) and Immunoquantification have successfully evolved to include the quantitation of 5hmC, 5fC and 5caC. Although the analytical performance of LC-MS/MS is superior, the simplicity afforded by the experimental procedure of immunoquantitation ensures it’s near ubiquity in clinical applications. Recent developments in spectroscopy, nanotechnology and sequencing also provide immense promise for future evaluations and are discussed briefly. Finally, we provide a perspective on the current scenario of global DNA methylation analysis tools and present suggestions to develop the next generation toolset.
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Affiliation(s)
- Basudev Chowdhury
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, 47907 IN USA
| | - Il-Hoon Cho
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam, 461-713 Republic of Korea
| | - Joseph Irudayaraj
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
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42
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A MoS₂ Nanosheet-Based Fluorescence Biosensor for Simple and Quantitative Analysis of DNA Methylation. SENSORS 2016; 16:s16101561. [PMID: 27669248 PMCID: PMC5087350 DOI: 10.3390/s16101561] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/24/2016] [Accepted: 07/06/2016] [Indexed: 12/28/2022]
Abstract
MoS2 nanomaterial has unique properties, including innate affinity with ss-DNA and quenching ability for fluorescence dyes. Here, we present the development of a simple fluorescence biosensor based on water-soluble MoS2 nanosheets and restriction endonuclease BstUI for methylation analysis of p16 promoter. The biosensing platform exhibited excellent sensitivity in detecting DNA with a linear range of 100 pM~20 nM and a detection limit of 140 pM. More importantly, our method could distinguish as low as 1% difference in methylation level. Compared with previous methylation analysis, our design is both time saving and simple to operate, avoiding the limitations of PCR-based assays without compromising performance.
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43
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Toehold-aided DNA recycling amplification using hemin and G-quadruplex reporter DNA on magnetic beads as tags for chemiluminescent determination of riboflavin. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1937-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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44
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Ma Y, Bai Y, Mao H, Hong Q, Yang D, Zhang H, Liu F, Wu Z, Jin Q, Zhou H, Cao J, Zhao J, Zhong X, Mao H. A panel of promoter methylation markers for invasive and noninvasive early detection of NSCLC using a quantum dots-based FRET approach. Biosens Bioelectron 2016; 85:641-648. [PMID: 27240011 DOI: 10.1016/j.bios.2016.05.067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 05/14/2016] [Accepted: 05/21/2016] [Indexed: 01/25/2023]
Abstract
Non-small-cell lung cancer (NSCLC) leads to a significant proportion of cancer-related deaths, and early detection of NSCLC can significantly increase cancer survival rates. A promising approach has been studied to exploit DNA methylation, which is closely correlated to early cancer diagnosis. Herein, in order to realize the early detection of NSCLC, we utilized the developed quantum dots-based (QDs-based) fluorescence resonance energy transfer (FRET) nanosensor technique to analyze the promoter methylation in early stage NSCLC tissue samples and noninvasive bronchial brushing specimens. Using this method, the methylation levels can be quantitatively determined by measuring the signal amplification during FRET. A panel of three tumor suppressor genes (PCDHGB6, HOXA9 and RASSF1A) was assessed in 50 paired early stage NSCLC and their adjacent nontumorous tissue (NT) samples, and 50 early stage NSCLC bronchial brushing and normal specimens. The combined detection was able to identify not only tissue samples but noninvasive bronchial brushing specimens from control cases with a high degree of sensitivity of 92% (AUC=0.977, P<0.001) and 80% (AUC=0.907, P<0.001) respectively, indicating the versatility of promoter expression in invasive and noninvasive NSCLC samples. Therefore this approach can be used to sensitively analyze the methylation levels of cancer-related genes, which might be a potential tool for noninvasive early clinical diagnosis of cancers.
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Affiliation(s)
- Yunfei Ma
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China; Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yanan Bai
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Hailei Mao
- Departments of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qunying Hong
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Dawei Yang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Honglian Zhang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Fangming Liu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Zhenhua Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Qinghui Jin
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Hongbo Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Jian Cao
- Department of Medicine/Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Xinhua Zhong
- Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, China.
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China.
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45
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Samanta S, Manna U, Ray T, Das G. An aggregation-induced emission (AIE) active probe for multiple targets: a fluorescent sensor for Zn(2+) and Al(3+) & a colorimetric sensor for Cu(2+) and F(-). Dalton Trans 2016; 44:18902-10. [PMID: 26467383 DOI: 10.1039/c5dt03186a] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A rationally designed probe L, which consists of both cation and anion binding sites, is capable of displaying interesting aggregation induced emission (AIE) properties. L not only can sense Al(3+) and Zn(2+) through selective turn-on fluorescence responses in 9 : 1 methanol-HEPES buffer (5 mM, pH 7.3; 9 : 1, v/v) medium due to metal ion triggered AIE activity, but also can distinguish them through individual emission signals. L can also detect Cu(2+) in mixed buffer medium and F(-) in acetonitrile through sharp colorimetric responses. All the sensing processes are conspicuous through the naked eye. A theoretical study strongly backed the proposed sensing mechanisms.
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Affiliation(s)
- Soham Samanta
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India.
| | - Utsab Manna
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India.
| | - Turjya Ray
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India.
| | - Gopal Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, India.
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46
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Lv F, Qiu T, Liu L, Ying J, Wang S. Recent Advances in Conjugated Polymer Materials for Disease Diagnosis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:696-705. [PMID: 26679834 DOI: 10.1002/smll.201501700] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 10/28/2015] [Indexed: 06/05/2023]
Abstract
The extraordinary optical amplification and light-harvesting properties of conjugated polymers impart sensing systems with higher sensitivity, which meets the primary demands of early cancer diagnosis. Recent advances in the detection of DNA methylation and mutation with polyfluorene derivatives based fluorescence resonance energy transfer (FRET) as a means to modulate fluorescent responses attest to the great promise of conjugated polymers as powerful tools for the clinical diagnosis of diseases. To facilitate the ever-changing needs of diagnosis, the development of detection approaches and FRET signal analysis are highlighted in this review. Due to their exceptional brightness, excellent photostability, and low or absent toxicity, conjugated polymers are verified as superior materials for in-vivo imaging, and provide feasibility for future clinical molecular-imaging applications. The integration of conjugated polymers with clinical research has shown profound effects on diagnosis for the early detection of disease-related biomarkers, as well as in-vivo imaging, which leads to a multidisciplinary scientific field with perspectives in both basic research and application issues.
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Affiliation(s)
- Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Tian Qiu
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, PR China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Jianming Ying
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, PR China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
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47
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Samanta S, Datta BK, Boral M, Nandan A, Das G. A multi-responsive turn-on flurogenic probe to sense Zn2+, Cd2+and Pb2+: left-right-center emission signal swing. Analyst 2016; 141:4388-93. [DOI: 10.1039/c6an00657d] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A rationally designed multi-target probe can sense Zn2+, Cd2+and Pb2+through individual TURN-ON emission signals in physiological pH with signal swing.
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Affiliation(s)
- Soham Samanta
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | | | - Madhurima Boral
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Abhijit Nandan
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Gopal Das
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
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48
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Zhang R, Lv W, Luan M, Zheng J, Shi M, Zhu H, Li J, Lv H, Zhang M, Shang Z, Duan L, Jiang Y. Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels. Oncotarget 2015; 6:40235-46. [PMID: 26515589 PMCID: PMC4741891 DOI: 10.18632/oncotarget.5504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/06/2015] [Indexed: 12/12/2022] Open
Abstract
Different human genes often exhibit different degrees of stability in their DNA methylation levels between tissues, samples or cell types. This may be related to the evolution of human genome. Thus, we compared the evolutionary conservation between two types of genes: genes with stable DNA methylation levels (SM genes) and genes with fluctuant DNA methylation levels (FM genes). For long-term evolutionary characteristics between species, we compared the percentage of the orthologous genes, evolutionary rate dn/ds and protein sequence identity. We found that the SM genes had greater percentages of the orthologous genes, lower dn/ds, and higher protein sequence identities in all the 21 species. These results indicated that the SM genes were more evolutionarily conserved than the FM genes. For short-term evolutionary characteristics among human populations, we compared the single nucleotide polymorphism (SNP) density, and the linkage disequilibrium (LD) degree in HapMap populations and 1000 genomes project populations. We observed that the SM genes had lower SNP densities, and higher degrees of LD in all the 11 HapMap populations and 13 1000 genomes project populations. These results mean that the SM genes had more stable chromosome genetic structures, and were more conserved than the FM genes.
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Affiliation(s)
- Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Meiwei Luan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Jiajia Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Miao Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Hongjie Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Jin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Mingming Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Lian Duan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
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Ma Y, Zhang H, Liu F, Wu Z, Lu S, Jin Q, Zhao J, Zhong X, Mao H. Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method. NANOSCALE 2015; 7:17547-17555. [PMID: 26446775 DOI: 10.1039/c5nr04956c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR amplification for the incorporation of Alexa Fluor-647 (A647) fluorophores. DNA methylation levels can be detected qualitatively through gel analysis and quantitatively by the signal amplification from QDs to A647 during FRET. Furthermore, the methylation levels of three tumor suppressor genes, PCDHGB6, HOXA9 and RASSF1A, in 20 lung adenocarcinoma and 20 corresponding adjacent nontumorous tissue (NT) samples were measured to verify the feasibility of the QD-based FRET method and a high sensitivity for cancer detection (up to 90%) was achieved. Our QD-based FRET method is a convenient, continuous and high-throughput method, and is expected to be an alternative for detecting DNA methylation as a biomarker for certain human cancers.
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Affiliation(s)
- Yunfei Ma
- Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, 200237, PR China.
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50
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Label-free electrochemical detection of methyltransferase activity and inhibitor screening based on endonuclease HpaII and the deposition of polyaniline. Biosens Bioelectron 2015; 73:188-194. [DOI: 10.1016/j.bios.2015.05.066] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 11/22/2022]
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