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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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Duprey JLHA, Bassani DM, Hyde EI, Jonusauskas G, Ludwig C, Rodger A, Spencer N, Vyle JS, Wilkie J, Zhao ZY, Tucker JHR. Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes. Org Biomol Chem 2018; 16:6576-6585. [DOI: 10.1039/c8ob01710g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.
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Affiliation(s)
| | - Dario M. Bassani
- Institut des Sciences Moléculaires, CNRS UMR 5255
- Université Bordeaux
- Talence 33405
- France
| | - Eva I. Hyde
- School of Biosciences
- The University of Birmingham
- Edgbaston
- UK
| | - Gediminas Jonusauskas
- Laboratoire Ondes et Matière d'Aquitaine
- UMR CNRS 5798
- Université Bordeaux
- Talence 33405
- France
| | - Christian Ludwig
- Henry Wellcome Building for Biomolecular NMR Spectroscopy
- Institute of Cancer & Genomic Sciences
- College of Medical & Dental Sciences
- University of Birmingham
- Edgbaston
| | - Alison Rodger
- Department of Molecular Sciences
- Faculty of Science and Engineering
- Macquarie University
- North Ryde
- Australia
| | - Neil Spencer
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
| | - Joseph S. Vyle
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
| | - John Wilkie
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
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Duprey JLHA, Bullen GA, Zhao ZY, Bassani DM, Peacock AFA, Wilkie J, Tucker JHR. Single Site Discrimination of Cytosine, 5-Methylcytosine, and 5-Hydroxymethylcytosine in Target DNA Using Anthracene-Tagged Fluorescent Probes. ACS Chem Biol 2016; 11:717-21. [PMID: 26580817 DOI: 10.1021/acschembio.5b00796] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The ability to discriminate between epigenetic variants in DNA is a necessary tool if we are to increase our understanding of the roles that they play in various biological processes and medical conditions. Herein, it is demonstrated how a simple two-step fluorescent probe assay can be used to differentiate all three major epigenetic variants of cytosine at a single locus site in a target strand of DNA.
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Affiliation(s)
- Jean-Louis H. A. Duprey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Gemma A. Bullen
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Zheng-yun Zhao
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Dario M. Bassani
- Univ. Bordeaux, CNRS, ISM UMR 5255 351, Cours de la Libération, 33400 Talence, France
| | - Anna F. A. Peacock
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - John Wilkie
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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Duprey JLHA, Carr-Smith J, Horswell SL, Kowalski J, Tucker JHR. Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA. J Am Chem Soc 2016; 138:746-9. [PMID: 26694542 DOI: 10.1021/jacs.5b11319] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.
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Affiliation(s)
- Jean-Louis H A Duprey
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - James Carr-Smith
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - Sarah L Horswell
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - Jarosław Kowalski
- Insitute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - James H R Tucker
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
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Sun H, Hou J, Shi W, Zhang L. Estrogen receptor 1 (ESR1) genetic variations in cancer risk: a systematic review and meta-analysis. Clin Res Hepatol Gastroenterol 2015; 39:127-35. [PMID: 25200861 DOI: 10.1016/j.clinre.2014.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/10/2014] [Accepted: 07/23/2014] [Indexed: 02/04/2023]
Abstract
BACKGROUND Emerging published data on the association between single nucleotide polymorphisms (SNPs) in the estrogen receptor 1 (ESR1) gene and cancer susceptibility are inconsistent. This review and meta-analysis is performed to derive a more precise evaluation of this relationship. METHODS The literature search of PubMed, Embase, Web of Science and CNKI databases was conducted from their inception through June 2014. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association. RESULTS Twenty-two literatures were enrolled in this meta-analysis. The results indicated that ESR1 rs1801132 (C>G) was associated with cancer risk in Caucasian populations. However, the results of stratified analysis by cancer type and source of controls indicated that no significant association was found. Furthermore, rs2077647 (A>G) was only associated with an increased risk of hepatocellular carcinoma, but was an adverse effect on cancer risk in Caucasian populations. CONCLUSIONS This present meta-analysis indicated that rs1801132 (C>G) and rs2077647 (A>G) may be protective factors in Caucasian populations. Meanwhile, rs2077647 (A>G) may be closely related with hepatocellular carcinoma.
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Affiliation(s)
- Huiling Sun
- Department of Life Sciences, Nanjing Normal University, Nanjing 210046, Jiangsu, China
| | - Jinjun Hou
- Clinical Laboratory, Mother and Child Health Care Hospital of Qixia District, Nanjing, Nanjing 210028, Jiangsu, China; Clinical Laboratory, The North Branch of Nanjing Mother and Child Health Care Hospital, Nanjing 210004, Jiangsu, China.
| | - Wenbin Shi
- Clinical Laboratory, Nanjing Traditional Chinese Medical Hospital, Nanjing 210001, Jiangsu, China
| | - Lei Zhang
- Department of Orthopaedics, Lanxi People's Hospital, Jinhua, 321100 Zhejiang, China
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Barthes NPF, Karpenko IA, Dziuba D, Spadafora M, Auffret J, Demchenko AP, Mély Y, Benhida R, Michel BY, Burger A. Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues. RSC Adv 2015. [DOI: 10.1039/c5ra02709h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.
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Affiliation(s)
- N. P. F. Barthes
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - I. A. Karpenko
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - D. Dziuba
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - M. Spadafora
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - J. Auffret
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | | | - Y. Mély
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
| | - R. Benhida
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - B. Y. Michel
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - A. Burger
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
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Dziuba D, Karpenko IA, Barthes NPF, Michel BY, Klymchenko AS, Benhida R, Demchenko AP, Mély Y, Burger A. Rational Design of a Solvatochromic Fluorescent Uracil Analogue with a Dual-Band Ratiometric Response Based on 3-Hydroxychromone. Chemistry 2014; 20:1998-2009. [DOI: 10.1002/chem.201303399] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Indexed: 12/24/2022]
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8
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Wang YM, Liu ZW, Guo JB, Wang XF, Zhao XX, Zheng X. ESR1 Gene Polymorphisms and Prostate Cancer Risk: A HuGE Review and Meta-Analysis. PLoS One 2013; 8:e66999. [PMID: 23805288 PMCID: PMC3689664 DOI: 10.1371/journal.pone.0066999] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 05/14/2013] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Many published data on the association between single nucleotide polymorphisms (SNPs) in the ESR1 gene and prostate cancer susceptibility are inconclusive. The aim of this Human Genome Epidemiology (HuGE) review and meta-analysis is to derive a more precise estimation of this relationship. METHODS A literature search of PubMed, Embase, Web of Science and Chinese Biomedical (CBM) databases was conducted from their inception through July 1st, 2012. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the strength of association. RESULTS Twelve case-control studies were included with a total 2,165 prostate cancer cases and 3,361 healthy controls. When all the eligible studies were pooled into the meta-analysis, ESR1 PvuII (C>T) and XbaI (A>G) polymorphisms showed no association with the risk of prostate cancer. However, in the stratified analyses based on ethnicity and country, the results indicated that ESR1 PvuII (C>T) polymorphism was significantly associated with increased risk of prostate cancer among Asian populations, especially among Indian population; while ESR1 XbaI (A>G) polymorphism may significantly increase the risk of prostate cancer among American population. Furthermore, we also performed a pooled analysis for all eligible case-control studies to explore the role of codon 10 (T>C), codon 325 (C>G), codon 594 (G>A) and +261G>C polymorphisms in prostate cancer risk. Nevertheless, no significant associations between these polymorphisms and the risk of prostate cancer were observed. CONCLUSION Results from the current meta-analysis indicate that ESR1 PvuII (C>T) polymorphism may be a risk factor for prostate cancer among Asian populations, especially among Indian population; while ESR1 XbaI (A>G) polymorphism may increase the risk of prostate cancer among American population.
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Affiliation(s)
- Yu-Mei Wang
- Department of Hospice, Shengjing Hospital of China Medical University, Shenyang, China
- * E-mail:
| | - Zu-Wang Liu
- Department of Hospice, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jing-Bo Guo
- Department of Hospice, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao-Fang Wang
- Department of Hospice, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xin-Xin Zhao
- Department of Hospice, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xuan Zheng
- Department of Hospice, Shengjing Hospital of China Medical University, Shenyang, China
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Manchester J, Bassani DM, Duprey JLHA, Giordano L, Vyle JS, Zhao ZY, Tucker JHR. Photocontrolled binding and binding-controlled photochromism within anthracene-modified DNA. J Am Chem Soc 2012; 134:10791-4. [PMID: 22694485 PMCID: PMC3614019 DOI: 10.1021/ja304205m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modified DNA strands undergo a reversible light-induced reaction involving the intramolecular photodimerization of two appended anthracene tags. The photodimers exhibit markedly different binding behavior toward a complementary strand that depends on the number of bases between the modified positions. By preforming the duplex, photochromism can be suppressed, illustrating dual-mode gated behavior.
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Affiliation(s)
- Jack Manchester
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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