1
|
Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering. Org Biomol Chem 2024; 22:3025-3034. [PMID: 38530278 DOI: 10.1039/d4ob00279b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.
Collapse
Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Clément Denhez
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, F-38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| |
Collapse
|
2
|
Bangruwa N, Srivastava M, Mishra D. CISS-Based Label-Free Novel Electrochemical Impedimetric Detection of UVC-Induced DNA Damage. ACS OMEGA 2022; 7:37705-37713. [PMID: 36312421 PMCID: PMC9609074 DOI: 10.1021/acsomega.2c04659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
In this work, we demonstrate chiral-induced spin selectivity (CISS)-based label-free electrochemical impedimetric detection of radiation-induced DNA damage using the electrons' spin as a novel tool of sensing. For this, self-assembled monolayers (SAMs) of short ds-DNA (of length 7.14 nm) are prepared on arrays of multilayer thin film devices comprising a gold overlay (500 μm diameter with 10 nm thickness) on a nickel thin film (100 nm) fabricated by the physical vapor deposition technique. Subsequently, the SAMs of ds-DNA are exposed to ultraviolet C (UVC) radiation for a prolonged period of 8 h to induce structural perturbations in DNA. The susceptibility of DNA to radiation-induced damage was probed by recording the spin-dependent electrochemical impedimetric spectra, wherein a continuous sinusoidal wave of the amplitude of 10 mV was superimposed on DC bias in the frequency range of 100-105 Hz, with simultaneous spin injection through the attached DNA. The inherent correlation between the charge-transfer resistance (R ct) and the spin selectivity of electrons through DNA was taken into account for the detection of DNA damage for the first time with a limit of detection achieved up to 10 picomolar concentrations of DNA. As the spin-polarized electrons directly probe the structural symmetry, it is robust against perturbation from electronic signals usually found in conventional electrochemical biosensors.
Collapse
Affiliation(s)
- Neeraj Bangruwa
- Department
of Physics and Astrophysics, University
of Delhi, New Delhi110007, India
| | - Manish Srivastava
- Department
of Chemical Engineering and Technology, Indian Institute of Technology, (BHU), Varanasi221005, India
| | - Debabrata Mishra
- Department
of Physics and Astrophysics, University
of Delhi, New Delhi110007, India
| |
Collapse
|
3
|
The Role of Posttranslational Modifications in DNA Repair. BIOMED RESEARCH INTERNATIONAL 2020. [DOI: 10.1155/2020/7493902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human body is a complex structure of cells, which are exposed to many types of stress. Cells must utilize various mechanisms to protect their DNA from damage caused by metabolic and external sources to maintain genomic integrity and homeostasis and to prevent the development of cancer. DNA damage inevitably occurs regardless of physiological or abnormal conditions. In response to DNA damage, signaling pathways are activated to repair the damaged DNA or to induce cell apoptosis. During the process, posttranslational modifications (PTMs) can be used to modulate enzymatic activities and regulate protein stability, protein localization, and protein-protein interactions. Thus, PTMs in DNA repair should be studied. In this review, we will focus on the current understanding of the phosphorylation, poly(ADP-ribosyl)ation, ubiquitination, SUMOylation, acetylation, and methylation of six typical PTMs and summarize PTMs of the key proteins in DNA repair, providing important insight into the role of PTMs in the maintenance of genome stability and contributing to reveal new and selective therapeutic approaches to target cancers.
Collapse
|
4
|
Jones NC, Nielsen SB, Hoffmann SV. On the delocalization length in RNA single strands of cytosine: how many bases see the light? Phys Chem Chem Phys 2020; 22:2188-2192. [DOI: 10.1039/c9cp05292e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics.
Collapse
Affiliation(s)
- Nykola C. Jones
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | | | | |
Collapse
|
5
|
Gekko K. Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview. Biophys Physicobiol 2019; 16:41-58. [PMID: 30923662 PMCID: PMC6435020 DOI: 10.2142/biophysico.16.0_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/13/2019] [Indexed: 12/01/2022] Open
Abstract
Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.
Collapse
Affiliation(s)
- Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| |
Collapse
|
6
|
Hassan N, Jalil A, Triwahyono S, Hitam C, Rahman A, Khusnun N, Mamat C, Asmadi M, Mohamed M, Ali M, Prasetyoko D. Exploiting copper–silica–zirconia cooperative interactions for the stabilization of tetragonal zirconia catalysts and enhancement of the visible-light photodegradation of bisphenol A. J Taiwan Inst Chem Eng 2018. [DOI: 10.1016/j.jtice.2017.10.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
7
|
Vinje J, Falck M, Mazzola F, Cooil SP, Koch H, Høyvik IM, Wells J. Tautomerization of Thymine Using Ultraviolet Light. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9666-9672. [PMID: 28835097 DOI: 10.1021/acs.langmuir.7b02473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultraviolet-light-induced changes to the nucleobase thymine deposited onto a MoS2 surface were studied using photoelectron spectroscopy and first-principles calculations. These measurements suggest changes in the molecular structure indicated by changes in core electron binding energies. The experimental work has been interpreted by means of ab initio calculations using coupled cluster singles and doubles (CCSD) linear response theory. Contrary to the expected behavior, i.e., the dimerization of two thymine molecules into a pyrimidine dimer, a shift between two tautomeric forms was observed upon UV-exposure. Exposure to ionizing radiation is known to induce damage in many biological molecules, and the present work gives additional insight into its effects on thymine, the interactions of the molecules, and finally how certain UV photoproducts may be avoided.
Collapse
Affiliation(s)
- Jakob Vinje
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Merete Falck
- NTNU Nanomechanical Lab, Department of Structural Engineering, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Federico Mazzola
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Simon Phillip Cooil
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Ida-Marie Høyvik
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Justin Wells
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| |
Collapse
|
8
|
Kudr J, Richtera L, Xhaxhiu K, Hynek D, Heger Z, Zitka O, Adam V. Carbon dots based FRET for the detection of DNA damage. Biosens Bioelectron 2017; 92:133-139. [PMID: 28213325 DOI: 10.1016/j.bios.2017.01.067] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 12/19/2022]
Abstract
Here, we aimed our attention at the synthesis of carbon dots (C-dots) with the ability to interact with DNA to suggest an approach for the detection of DNA damage. Primarily, C-dots modified with amine moieties were synthesized using the one-step microwave pyrolysis of citric acid in the presence of diethylenetriamine. The C-dots showed strong photoluminescence with a quantum yield of 4%. In addition, the C-dots (2.8±0.8nm) possessed a good colloidal stability and exhibited a positive surface charge (ζ=36mV) at a neutral pH. An interaction study of the C-dots and the DNA fragment of λ bacteriophage was performed, and the DNA binding resulted in changes to the photoluminescent and absorption properties of the C-dots. A binding of the C-dots to DNA was also observed as a change to DNA electrophoretic mobility and a decreased ability to intercalate ethidium bromide (EtBr). Moreover, the Förster (or fluorescence) resonance energy transfer (FRET) between the C-dots and EtBr was studied, in which the C-dots serve as an excitation energy donor and the EtBr serves as an acceptor. When DNA was damaged using ultraviolet (UV) radiation (λ=254nm) and hydroxyl radicals, the intensity of the emitted photoluminescence at 612nm significantly decreased. The concept was proved on analysis of the genomic DNA from PC-3 cells and DNA isolated from melanoma tissues.
Collapse
Affiliation(s)
- Jiri Kudr
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czechia
| | - Kledi Xhaxhiu
- Department of Chemistry, Faculty of Natural Sciences, University of Tirana, Blv. Zog I, No. 2/1, 1001 Tirana, Albania
| | - David Hynek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czechia
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czechia
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czechia
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czechia.
| |
Collapse
|