1
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Saleem M, Hanif M, Rafiq M, Ali A, Raza H, Kim SJ, Lu C. Recent Development on Sensing Strategies for Small Molecules Detections. J Fluoresc 2024; 34:1493-1525. [PMID: 37644375 DOI: 10.1007/s10895-023-03387-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Sensors play a critical role in the detection and monitoring of various substances present in our environment, providing us with valuable information about the world around us. Within the field of sensor development, one area that holds particular importance is the detection of small molecules. Small molecules encompass a wide range of organic or inorganic compounds with low molecular weight, typically below 900 Daltons including gases, volatile organic compounds, solvents, pesticides, drugs, biomarkers, toxins, and pollutants. The accurate and efficient detection of these small molecules has attracted significant interest from the scientific community due to its relevance in diverse fields such as environmental pollutants monitoring, medical diagnostics, industrial optimization, healthcare remedies, food safety, ecosystems, and aquatic and terrestrial life preservation. To meet the demand for precise and efficient monitoring of small molecules, this summary aims to provide an overview of recent advancements in sensing and quantification strategies for various organic small molecules including Hydrazine, Glucose, Morpholine, Ethanol amine, Nitrosamine, Oxygen, Nitro-aromatics, Phospholipids, Carbohydrates, Antibiotics, Pesticides, Drugs, Adenosine Triphosphate, Aromatic Amine, Glutathione, Hydrogen Peroxide, Acetone, Methyl Parathion, and Thiophenol. The focus is on understanding the receptor sensing mechanism, along with the electrical, optical, and electrochemical response. Additionally, the variations in UV-visible spectral properties of the ligands upon treatment with the receptor, fluorescence and absorption titration analysis for limit of detection (LOD) determination, and bioimaging analysis are discussed wherever applicable. It is anticipated that the information gathered from this literature survey will be helpful for the perusal of innovation regarding sensing strategies.
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Affiliation(s)
- Muhammad Saleem
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan.
- Department of Chemistry, Thal University Bhakkar, Punjab, 30000, Bhakkar, Pakistan.
| | - Muhammad Hanif
- Department of Chemistry, GC University Faisalabad, Sub Campus Layyah-31200, Layyah, Pakistan
| | - Muhammad Rafiq
- Department of Physiology and Biochemistry, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 6300, Pakistan
| | - Anser Ali
- Department of Zoology, Mirpur University of Science and Technology (MUST), Mirpur, 10250, Pakistan
| | - Hussain Raza
- Department of Biological Sciences, Kongju National University, Kongju, Chungnam, Republic of Korea
| | - Song Ja Kim
- Department of Biological Sciences, Kongju National University, Kongju, Chungnam, Republic of Korea
| | - Changrui Lu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, 201620, China
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2
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Kılıç M, Diamantis P, Johnson SK, Toth O, Rothlisberger U. Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:8434-8445. [PMID: 37963372 PMCID: PMC10687876 DOI: 10.1021/acs.jctc.3c01013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation by roughly 1 eV, which is very similar to what was recently reported for free native and 8oxoG-containing DNA. In contrast, the effect of 8oxoG on the reorganization free energy is even smaller for packed DNA (decrease of 0.13 and 0.01 eV for defect-free and defect-containing systems, respectively) compared to the one for free DNA (0.25 eV), consistent with the increased rigidity of the NCP as compared to free DNA. Furthermore, the presence of an 8oxoG defect does not yield any significant changes in the packed DNA structure. Such a conclusion favors the idea that in the case of chromatin, defect-induced changes in DNA redox chemistry can also be exploited to detect damaged bases via DNA-mediated hole transfer.
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Affiliation(s)
| | | | - Sophia K. Johnson
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Oliver Toth
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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3
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Chandra S, Williams A, Maksudov F, Kliuchnikov E, Pattiya Arachchillage KGG, Piscitelli P, Castillo A, Marx KA, Barsegov V, Artes Vivancos JM. Charge transport in individual short base stacked single-stranded RNA molecules. Sci Rep 2023; 13:19858. [PMID: 37963922 PMCID: PMC10645971 DOI: 10.1038/s41598-023-46263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking. These ssRNA sequences show single-molecule conductance values around [Formula: see text] ([Formula: see text]), while equivalent-length ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT pathway. In contrast, DNA and a control RNA sequence without significant base-stacking tend to form closed structures and thus are incapable of efficient CT.
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Affiliation(s)
- Subrata Chandra
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Ajoke Williams
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | | | | | - Patrick Piscitelli
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Aderlyn Castillo
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA.
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Cai Y, Lv L, Lu T, Ding M, Yu Z, Chen X, Zhou X, Wang X. α-KG inhibits tumor growth of diffuse large B-cell lymphoma by inducing ROS and TP53-mediated ferroptosis. Cell Death Discov 2023; 9:182. [PMID: 37308557 DOI: 10.1038/s41420-023-01475-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 06/14/2023] Open
Abstract
Metabolic reprogramming is a hallmark of human malignancies. Dysregulation of glutamine metabolism is essential for tumorigenesis, microenvironment remodeling, and therapeutic resistance. Based on the untargeted metabolomics sequencing, we identified that the glutamine metabolic pathway was up-regulated in the serum of patients with primary DLBCL. High levels of glutamine were associated with inferior clinical outcomes, indicative of the prognostic value of glutamine in DLBCL. In contrast, the derivate of glutamine alpha-ketoglutarate (α-KG) was negatively correlated with the invasiveness features of DLBCL patients. Further, we found that treatment with the cell-permeable derivative of α-KG, known as DM-αKG, significantly suppressed tumor growth by inducing apoptosis and non-apoptotic cell death. Accumulation of a-KG promoted oxidative stress in double-hit lymphoma (DHL), which depended on malate dehydrogenase 1 (MDH1)-mediated 2-hydroxyglutarate (2-HG) conversion. High levels of reactive oxygen species (ROS) contributed to ferroptosis induction by promoting lipid peroxidation and TP53 activation. In particular, TP53 overexpression derived from oxidative DNA damage, further leading to the activation of ferroptosis-related pathways. Our study demonstrated the importance of glutamine metabolism in DLBCL progression and highlighted the potential application of α-KG as a novel therapeutic strategy for DHL patients.
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Affiliation(s)
- Yiqing Cai
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Liemei Lv
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Tiange Lu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Mengfei Ding
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Zhuoya Yu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiaomin Chen
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiangxiang Zhou
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
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Wan J, Brož B, Liu Y, Huang SR, Marek A, Tureček F. The DNA Radical Code. Resolution of Identity in Dissociations of Trinucleotide Codon Cation Radicals in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:304-319. [PMID: 36596259 DOI: 10.1021/jasms.2c00322] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Sixty DNA trinucleotide cation radicals covering a large part of the genetic code alphabet were generated by electron transfer in the gas phase, and their chemistry was studied by collision-induced dissociation tandem mass spectrometry and theoretical calculations. The major dissociations involved loss of nucleobase molecules and radicals, backbone cleavage, and cross-ring fragmentations that depended on the nature and position of the nucleobases. Mass identity in dissociations of symmetrical trinucleotide cation radicals of the (XXX+2H)+• and (XYX+2H)+• type was resolved by specific 15N labeling. The specific features of trinucleotide cation radical dissociations involved the dominant formation of d2+ ions, hydrogen atom migrations accompanying the formation of (w2+H)+•, (w2+2H)+, and (d2+2H)+ sequence ions, and cross-ring cleavages in the 3'- and 5'-deoxyribose moieties that depended on the nucleobase type and its position in the ion. Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations were used to obtain structures and energies of several cation-radical protomers and conformers for (AAA+2H)+•, (CCC+2H)+•, (GGG+2H)+•, (ACA+2H)+•, and (CAA+2H)+• that were representative of the different types of backbone dissociations. The ion electronic structure, protonation and radical sites, and hydrogen bonding were used to propose reaction mechanisms for the dissociations.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Břetislav Brož
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Yue Liu
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Shu R Huang
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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6
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Qu W, Guo T, Yang B, Tian R, Qiu S, Chen X, Geng Z, Wang Z. Tracking HOCl by an incredibly simple fluorescent probe with AIE plus ESIPT in vitro and in vivo. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121649. [PMID: 35872428 DOI: 10.1016/j.saa.2022.121649] [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: 05/20/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Hypochlorous acid is an important active substance involved in a variety of physiological processes in living organisms, while abnormal concentrations of HOCl are strongly associated with a variety of diseases such as cancer, inflammation, atherosclerosis, and Alzheimer's disease. As a result, it's crucial to establish a reliable method for tracking HOCl in vivo in order to investigate its physiological consequences. In this work, we developed a fluorescent probe DFSN with both AIE and ESIPT for imaging HOCl in vivo. DFSN not only has a basic structure and is easy to synthesize, but also has superior performance. The probe responds to HOCl in less than 10 s and has good selectivity and sensitivity to HOCl (DL = 6.3 nM), with a 110-fold increase in fluorescence intensity following response. In addition, DFSN can realize the rapid detection of hypochlorous acid with naked eyes. Moreover, DFSN can be used for the detection of exogenous and endogenous HOCl in RAW264.7 cells, and additionally enables the tracking of HOCl in cancer cells (Hela cells and HepG2 cells). More notably, it has been utilized to image hypochlorous acid in zebrafish with great success. The probe DFSN will be useful in determining the physiological significance of HOCl.
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Affiliation(s)
- Wangbo Qu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China
| | - Taiyu Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China
| | - Bin Yang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China
| | - Ruowei Tian
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China
| | - Shuang Qiu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China
| | - Xinyue Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China
| | - Zhirong Geng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China.
| | - Zhilin Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210023, PR China.
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7
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Huang SR, Tureček F. Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization. J Phys Chem A 2022; 126:2480-2497. [PMID: 35439003 DOI: 10.1021/acs.jpca.2c00894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion-electron recombination energies (REad) for the lowest-energy isomers 2'-deoxy-(N-3H)adenos-1'-yl (4.74 eV), 2'-deoxy-(N-7H)guanos-1'-yl (4.66 eV), 2'-deoxy-(N-3H)cytid-1'-yl (5.12 eV), and 2'-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2'-deoxyadenosine, 2'-deoxy guanosine, 2'-deoxy cytidine, and 2'-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born-Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+· to A in both dAT+· and dA⊂dT+·, leading to charge and radical separation. Noncanonical T+· in dCT+· and dTC+· initiated rapid proton transfer to cytosine, whereas the canonical dCT+· dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+· and dG⊂dC+· containing canonical neutral and noncanonical ionized deoxycytidine.
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Affiliation(s)
- Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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8
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Sankar K, Baer R, Grazon C, Sabatelle RC, Lecommandoux S, Klapperich CM, Galagan JE, Grinstaff MW. An Allosteric Transcription Factor DNA-Binding Electrochemical Biosensor for Progesterone. ACS Sens 2022; 7:1132-1137. [PMID: 35412319 PMCID: PMC9985479 DOI: 10.1021/acssensors.2c00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe an electrochemical strategy to transduce allosteric transcription factor (aTF) binding affinity to sense steroid hormones. Our approach utilizes square wave voltammetry to monitor changes in current output as a progesterone (PRG)-specific aTF (SRTF1) unbinds from the cognate DNA sequence in the presence of PRG. The sensor detects PRG in artificial urine samples with sufficient sensitivity suitable for clinical applications. Our results highlight the capability of using aTFs as the biorecognition elements to develop electrochemical point-of-care biosensors for the detection of small-molecule biomarkers and analytes.
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Affiliation(s)
- Karthika Sankar
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA
| | - R Baer
- Department of Microbiology, Boston University, Boston, MA 02215, USA
| | - Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France.,University Bordeaux, Institut des Sciences Moléculaires (CNRS UMR 5255), 33405 Talence, France
| | - Robert C. Sabatelle
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Catherine M. Klapperich
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James E. Galagan
- Department of Microbiology, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
| | - Mark W. Grinstaff
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
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9
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Linke R, Limmer M, Juranek SA, Heine A, Paeschke K. The Relevance of G-Quadruplexes for DNA Repair. Int J Mol Sci 2021; 22:12599. [PMID: 34830478 PMCID: PMC8620898 DOI: 10.3390/ijms222212599] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/28/2023] Open
Abstract
DNA molecules can adopt a variety of alternative structures. Among these structures are G-quadruplex DNA structures (G4s), which support cellular function by affecting transcription, translation, and telomere maintenance. These structures can also induce genome instability by stalling replication, increasing DNA damage, and recombination events. G-quadruplex-driven genome instability is connected to tumorigenesis and other genetic disorders. In recent years, the connection between genome stability, DNA repair and G4 formation was further underlined by the identification of multiple DNA repair proteins and ligands which bind and stabilize said G4 structures to block specific DNA repair pathways. The relevance of G4s for different DNA repair pathways is complex and depends on the repair pathway itself. G4 structures can induce DNA damage and block efficient DNA repair, but they can also support the activity and function of certain repair pathways. In this review, we highlight the roles and consequences of G4 DNA structures for DNA repair initiation, processing, and the efficiency of various DNA repair pathways.
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Affiliation(s)
- Rebecca Linke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michaela Limmer
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Stefan A. Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
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10
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Diamantis P, Tavernelli I, Rothlisberger U. Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:6690-6701. [PMID: 32926773 DOI: 10.1021/acs.jctc.0c00568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. The quantum region of the native fragment comprised 3 G-C base pairs, while one G was replaced by an 8oxoG in the defect fragment. The calculated values for the redox free energy are 6.55 ± 0.28 eV and 5.62 ± 0.30 eV for the native and the 8oxoG-containing fragment, respectively. The respective estimates for the reorganization free energy are 1.25 ± 0.18 eV and 1.00 ± 0.18 eV. Both reactions follow the Marcus theory for electron transfer. The large difference in redox potential between the two fragments shows that replacement of a G by an 8oxoG renders the DNA more easily oxidizable. This finding is in agreement with the suggestion that DNA fragments containing an 8oxoG defect can act as sinks of oxidative damage that protect the rest of the genome from assault. In addition, the difference in redox potential between the native and the defect DNA fragment indicates that a charge transfer-based mechanism for the recognition of DNA defects might be feasible, in line with recent suggestions based on experimental observations.
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Affiliation(s)
- Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
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11
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Bag S, Aggarwal A, Maiti PK. Machine Learning Prediction of Electronic Coupling between the Guanine Bases of DNA. J Phys Chem A 2020; 124:7658-7664. [DOI: 10.1021/acs.jpca.0c04368] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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12
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Tóth Z, Kubečka J, Muchová E, Slavíček P. Ionization energies in solution with the QM:QM approach. Phys Chem Chem Phys 2020; 22:10550-10560. [PMID: 32010902 DOI: 10.1039/c9cp06154a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We discuss a fragment-based QM:QM scheme as a practical way to access the energetics of vertical electronic processes in the condensed phase. In the QM:QM scheme, we decompose the large molecular system into small fragments, which interact solely electrostatically. The energies of the fragments are calculated in a self-consistent field generated by the other fragments and the total energy of the system is calculated as a sum of the fragment energies. We show on two test cases (cytosine and a sodium cation) that the method allows one to accurately simulate the shift of vertical ionization energies (VIE) while going from the gas phase to the bulk. For both examples, the predicted solvent shifts and peak widths estimated at the DFT level agree well with the experimental observations. We argue that the QM:QM approach is more suitable than either an electrostatic embedding based QM/MM approach, a full quantum description at the DFT level with a generally used functional or a combination of both. We also discuss the potential scope of the applicability for other electronic processes such as Auger decay.
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Affiliation(s)
- Zsuzsanna Tóth
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague 6, Czech Republic.
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13
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Peng B, Kowalski K, Panyala A, Krishnamoorthy S. Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments. J Chem Phys 2020; 152:011101. [DOI: 10.1063/1.5138658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Bo Peng
- Advanced Computing, Mathematics, and Data Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Ajay Panyala
- High Performance Computing, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Sriram Krishnamoorthy
- High Performance Computing, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
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14
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Huang K, Li Y, Shim AR, Virk RKA, Agrawal V, Eshein A, Nap RJ, Almassalha LM, Backman V, Szleifer I. Physical and data structure of 3D genome. SCIENCE ADVANCES 2020; 6:eaay4055. [PMID: 31950084 PMCID: PMC6954067 DOI: 10.1126/sciadv.aay4055] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 11/20/2019] [Indexed: 05/05/2023]
Abstract
With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topology of DNA double helix. These functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi-self-similar manner, as revealed by our electron and optical imaging. Our multiscale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.
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Affiliation(s)
- Kai Huang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Corresponding author. (K.H.); (V.B.); (I.S.)
| | - Yue Li
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
| | - Anne R. Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Ranya K. A. Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Adam Eshein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Rikkert J. Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Corresponding author. (K.H.); (V.B.); (I.S.)
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Corresponding author. (K.H.); (V.B.); (I.S.)
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15
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Ferapontova EE. Electron Transfer in DNA at Electrified Interfaces. Chem Asian J 2019; 14:3773-3781. [PMID: 31545875 DOI: 10.1002/asia.201901024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/22/2019] [Indexed: 12/24/2022]
Abstract
The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, 8000, Aarhus C, Denmark
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16
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Pucci F, Rooman M. Relation between DNA ionization potentials, single base substitutions and pathogenic variants. BMC Genomics 2019; 20:551. [PMID: 31307386 PMCID: PMC6631442 DOI: 10.1186/s12864-019-5867-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background It is nowadays clear that single base substitutions that occur in the human genome, of which some lead to pathogenic conditions, are non-random and influenced by their flanking nucleobase sequences. However, despite recent progress, the understanding of these "non-local" effects is still far from being achieved. Results To advance this problem, we analyzed the relationship between the base mutability in specific gene regions and the electron hole transport along the DNA base stacks, as it is one of the mechanisms that have been suggested to contribute to these effects. More precisely, we studied the connection between the normalized frequency of single base substitutions and the vertical ionization potential of the base and its flanking sequence, estimated using MP2/6-31G* ab initio quantum chemistry calculations. We found a statistically significant overall anticorrelation between these two quantities: the lower the vIP value, the more probable the substitution. Moreover, the slope of the regression lines varies. It is larger for introns than for exons and untranslated regions, and for synonymous than for missense substitutions. Interestingly, the correlation appears to be more pronounced when considering the flanking sequence of the substituted base in the 3’ rather than in the 5’ direction, which corresponds to the preferred direction of charge migration. A weaker but still statistically significant correlation is found between the ionization potentials and the pathogenicity of the base substitutions. Moreover, pathogenicity is also preferentially associated with larger changes in ionization potentials upon base substitution. Conclusions With this analysis we gained new insights into the complex biophysical mechanisms that are at the basis of mutagenesis and pathogenicity, and supported the role of electron-hole transport in these matters. Electronic supplementary material The online version of this article (10.1186/s12864-019-5867-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave. 50, Bruxelles, 1050, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave. 50, Bruxelles, 1050, Belgium.
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17
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Diamantis P, Tavernelli I, Rothlisberger U. Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair. J Chem Theory Comput 2019; 15:2042-2052. [PMID: 30681847 DOI: 10.1021/acs.jctc.8b00645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as for larger fragments containing one or multiple pairs. Absolute values of VIE and VEA under implicit solvation did not converge as a function of model size even up to the largest systems taken into consideration (3 base pairs/2 nucleotide pairs). Nonetheless, a consistent trend was observed for the relative difference in the VIE of native and damaged DNA showing that the defect was lowering the VIE by -0.1 eV for the largest fragments. This strongly suggests that the presence of 8OG makes the DNA more easily oxidizable and is in line with experimental evidence that a defect region can act as a sink of oxidative damage. In contrast, relative differences in VEA were very small and varied inconsistently around 0.01 eV. This seems to indicate that insertion of 8OG has a negligible effect on the electron capturing properties of DNA. Similar conclusions can be drawn by the adiabatic IEs and EAs computed for some of the larger fragments. Analysis of the hole and excess electron distributions was consistent with the above trends. The findings presented here support the possibility that a mechanism based on hole transport through DNA may be efficiently employed by the cell for the detection of defect bases.
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Affiliation(s)
- Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , Swiss Federal Institute of Technology, CH-1015 Lausanne , Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , Swiss Federal Institute of Technology, CH-1015 Lausanne , Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , Swiss Federal Institute of Technology, CH-1015 Lausanne , Switzerland
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18
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Imran H, Manikandan PN, Dharuman V. Ultra-sensitive and selective label free electrochemical DNA detection at layer-by-layer self-assembled graphene oxide and vesicle liposome nano-architecture. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Tse EM, Zwang TJ, Bedoya S, Barton JK. Effective Distance for DNA-Mediated Charge Transport between Repair Proteins. ACS CENTRAL SCIENCE 2019; 5:65-72. [PMID: 30693326 PMCID: PMC6346725 DOI: 10.1021/acscentsci.8b00566] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 05/23/2023]
Abstract
The stacked aromatic base pairs within the DNA double helix facilitate charge transport down its length in the absence of lesions, mismatches, and other stacking perturbations. DNA repair proteins containing [4Fe4S] clusters can take advantage of DNA charge transport (CT) chemistry to scan the genome for mistakes more efficiently. Here we examine the effective length over which charge can be transported along DNA between these repair proteins. We define the effective CT distance as the length of DNA within which two proteins are able to influence their ensemble affinity to the DNA duplex via CT. Endonuclease III, a DNA repair glycosylase containing a [4Fe4S] cluster, was incubated with DNA duplexes of different lengths (1.5-9 kb), and atomic force microscopy was used to quantify the binding of proteins to these duplexes to determine how the relative protein affinity changes with increasing DNA length. A sharp change in binding slope is observed at 3509 base pairs, or about 1.2 μm, that supports the existence of two regimes for protein binding, one within the range for DNA CT, one outside of the range for CT; DNA CT between the redox proteins bound to DNA effectively decreases the ensemble binding affinity of oxidized and reduced proteins to DNA. Utilizing an Endonuclease III mutant Y82A, which is defective in carrying out DNA CT, shows only one regime for protein binding. Decreasing the temperature to 4 °C or including metallointercalators on the duplex, both of which should enhance base stacking and decrease DNA floppiness, leads to extending the effective length for DNA charge transport to ∼5300 bp or 1.8 μm. These results thus support DNA charge transport between repair proteins over kilobase distances. The results furthermore highlight the ability of DNA repair proteins to search the genome quickly and efficiently using DNA charge transport chemistry.
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20
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Teo RD, Smithwick ER, Migliore A, Beratan DN. A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation. Chem Commun (Camb) 2019; 55:206-209. [PMID: 30520908 DOI: 10.1039/c8cc09048c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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21
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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22
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Takahashi S, Kim KT, Podbevšek P, Plavec J, Kim BH, Sugimoto N. Recovery of the Formation and Function of Oxidized G-Quadruplexes by a Pyrene-Modified Guanine Tract. J Am Chem Soc 2018; 140:5774-5783. [PMID: 29608858 DOI: 10.1021/jacs.8b01577] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases in the G-quadruplex (G4) are sensitive to damage by oxidation, resulting in transformation to 8-oxo-7,8-dihydroguanine (8-oxoG). Because the formation of G4 represses the expression of some cancer-related genes, the presence of 8-oxoG in a G4 sequence might affect G4 formation and induce cancer progression. Thus, oxidized-G4 formation must be controlled using a chemical approach. In the present study, we investigated the effect of introduction of 8-oxoG into a G4 sequence on the formation and function of the G4 structure. The 8-oxoG-containing G4 derived from the promoter region of the human vascular endothelial growth factor ( VEGF) gene differed topologically from unoxidized G4. The oxidized VEGF G4 did not act as a replication block and was not stabilized by the G4-binding protein nucleolin. To recover G4 function, we developed an oligonucleotide consisting of a pyrene-modified guanine tract that replaces the oxidized guanine tract and forms stable intermolecular G4s with the other intact guanine tracts. When this oligonucleotide was used, the oxidized G4 stalled replication and was stabilized by nucleolin as with the unmodified G4. This strategy generally enables recovery of the function of any oxidized G4s and therefore has potential for cancer therapy.
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Affiliation(s)
| | - Ki Tae Kim
- Department of Chemistry, Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , Republic of Korea
| | - Peter Podbevšek
- Slovenian NMR Center , National Institute of Chemistry , SI-1000 Ljubljana , Slovenia
| | - Janez Plavec
- Slovenian NMR Center , National Institute of Chemistry , SI-1000 Ljubljana , Slovenia
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , Republic of Korea
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23
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Elfwing A, Cai W, Ouyang L, Liu X, Xia Y, Tang Z, Inganäs O. DNA Based Hybrid Material for Interface Engineering in Polymer Solar Cells. ACS APPLIED MATERIALS & INTERFACES 2018; 10:9579-9586. [PMID: 29505234 DOI: 10.1021/acsami.7b17807] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A new solution processable electron transport material (ETM) is introduced for use in photovoltaic devices, which consists of a metallic conjugated polyelectrolyte, poly(4-(2,3-dihydrothieno[3,4- b][1,4]dioxin-2-yl-methoxy)-1-butanesulfonic acid (PEDOT-S), and surfactant-functionalized deoxyribonucleic acid (DNA) (named DNA:CTMA:PEDOT-S). This ETM is demonstrated to effectively work for bulk-heterojunction organic photovoltaic devices (OPV) based on different electron acceptor materials. The fill factor, the open circuit voltage, and the overall power conversion efficiency of the solar cells with a DNA:CTMA:PEDOT-S modified cathode are comparable to those of devices with a traditional lithium fluoride/aluminum cathode. The new electron transport layer has high optical transmittance, desired work function and selective electron transport. A dipole effect induced by the use of the surfactant cetyltrimethylammonium chloride (CTMA) is responsible for lowering the electrode work function. The DNA:CTMA complex works as an optical absorption dilutor, while PEDOT-S provides the conducting pathway for electron transport, and allows thicker layer to be used, enabling printing. This materials design opens a new pathway to harness and optimize the electronic and optical properties of printable interface materials.
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Affiliation(s)
- Anders Elfwing
- Biomolecular and Organic Electronics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Wanzhu Cai
- Biomolecular and Organic Electronics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Liangqi Ouyang
- Biomolecular and Organic Electronics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Xianjie Liu
- Surface Physics and Chemistry Division, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Yuxin Xia
- Biomolecular and Organic Electronics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Zheng Tang
- Dresden Integrated Center for Applied Physics and Photonic Materials (IAPP) and Institute for Applied Physics , Technische Universität Dresden , Nöthnitzer Str. 61 , 01187 Dresden , Germany
| | - Olle Inganäs
- Biomolecular and Organic Electronics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
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24
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Sun CL, Liu LP, Tian F, Ding F, Wang LW. Charge-patching method for the calculation of electronic structure of polypeptides. Phys Chem Chem Phys 2018; 20:23301-23310. [DOI: 10.1039/c8cp01803k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the CPM method, the charge densities of polypeptides can be generated and their electronic structure can be further calculated.
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Affiliation(s)
- Chang-Liang Sun
- Center of Physical Chemistry Test
- Shenyang University of Chemical Technology
- Shenyang 110142
- People's Republic of China
- Materials Science Division
| | - Li-Ping Liu
- Materials Science Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- School of Physics
| | - Fubo Tian
- Materials Science Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- College of Physics
| | - Fu Ding
- Center of Physical Chemistry Test
- Shenyang University of Chemical Technology
- Shenyang 110142
- People's Republic of China
| | - Lin-Wang Wang
- Materials Science Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
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25
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Ba X, Boldogh I. 8-Oxoguanine DNA glycosylase 1: Beyond repair of the oxidatively modified base lesions. Redox Biol 2017; 14:669-678. [PMID: 29175754 PMCID: PMC5975208 DOI: 10.1016/j.redox.2017.11.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/08/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress and the resulting damage to genomic DNA are inevitable consequences of endogenous physiological processes, and they are amplified by cellular responses to environmental exposures. One of the most frequent reactions of reactive oxygen species with DNA is the oxidation of guanine to pre-mutagenic 8-oxo-7,8-dihydroguanine (8-oxoG). Despite the vulnerability of guanine to oxidation, vertebrate genes are primarily embedded in GC-rich genomic regions, and over 72% of the promoters of human genes belong to a class with a high GC content. In the promoter, 8-oxoG may serve as an epigenetic mark, and when complexed with the oxidatively inactivated repair enzyme 8-oxoguanine DNA glycosylase 1, provide a platform for the coordination of the initial steps of DNA repair and the assembly of the transcriptional machinery to launch the prompt and preferential expression of redox-regulated genes. Deviations/variations from this artful coordination may be the etiological links between guanine oxidation and various cellular pathologies and diseases during ageing processes.
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Affiliation(s)
- Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Science, Northeast Normal University, Changchun, Jilin 130024, China.
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.
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26
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Tse ECM, Zwang TJ, Barton JK. The Oxidation State of [4Fe4S] Clusters Modulates the DNA-Binding Affinity of DNA Repair Proteins. J Am Chem Soc 2017; 139:12784-12792. [PMID: 28817778 PMCID: PMC5929122 DOI: 10.1021/jacs.7b07230] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A central question important to understanding DNA repair is how certain proteins are able to search for, detect, and fix DNA damage on a biologically relevant time scale. A feature of many base excision repair proteins is that they contain [4Fe4S] clusters that may aid their search for lesions. In this paper, we establish the importance of the oxidation state of the redox-active [4Fe4S] cluster in the DNA damage detection process. We utilize DNA-modified electrodes to generate repair proteins with [4Fe4S] clusters in the 2+ and 3+ states by bulk electrolysis under an O2-free atmosphere. Anaerobic microscale thermophoresis results indicate that proteins carrying [4Fe4S]3+ clusters bind to DNA 550 times more tightly than those with [4Fe4S]2+ clusters. The measured increase in DNA-binding affinity matches the calculated affinity change associated with the redox potential shift observed for [4Fe4S] cluster proteins upon binding to DNA. We further devise an electrostatic model that shows this change in DNA-binding affinity of these proteins can be fully explained by the differences in electrostatic interactions between DNA and the [4Fe4S] cluster in the reduced versus oxidized state. We then utilize atomic force microscopy (AFM) to demonstrate that the redox state of the [4Fe4S] clusters regulates the ability of two DNA repair proteins, Endonuclease III and DinG, to bind preferentially to DNA duplexes containing a single site of DNA damage (here a base mismatch) which inhibits DNA charge transport. Together, these results show that the reduction and oxidation of [4Fe4S] clusters through DNA-mediated charge transport facilitates long-range signaling between [4Fe4S] repair proteins. The redox-modulated change in DNA-binding affinity regulates the ability of [4Fe4S] repair proteins to collaborate in the lesion detection process.
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Affiliation(s)
- Edmund C. M. Tse
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodore J. Zwang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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27
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Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 771:99-127. [PMID: 28342455 DOI: 10.1016/j.mrrev.2017.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 02/07/2023]
Abstract
Endogenous and exogenous reactive species cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. As a result, a plethora of mutagenic and/or cytotoxic products are formed in cellular DNA. This type of DNA damage is repaired by base excision repair, although nucleotide excision repair also plays a limited role. DNA glycosylases remove modified DNA bases from DNA by hydrolyzing the glycosidic bond leaving behind an apurinic/apyrimidinic (AP) site. Some of them also possess an accompanying AP-lyase activity that cleaves the sugar-phosphate chain of DNA. Since the first discovery of a DNA glycosylase, many studies have elucidated the mechanisms of action, substrate specificities and excision kinetics of these enzymes present in all living organisms. For this purpose, most studies used single- or double-stranded oligodeoxynucleotides with a single DNA lesion embedded at a defined position. High-molecular weight DNA with multiple base lesions has been used in other studies with the advantage of the simultaneous investigation of many DNA base lesions as substrates. Differences between the substrate specificities and excision kinetics of DNA glycosylases have been found when these two different substrates were used. Some DNA glycosylases possess varying substrate specificities for either purine-derived lesions or pyrimidine-derived lesions, whereas others exhibit cross-activity for both types of lesions. Laboratory animals with knockouts of the genes of DNA glycosylases have also been used to provide unequivocal evidence for the substrates, which had previously been found in in vitro studies, to be the actual substrates in vivo as well. On the basis of the knowledge gained from the past studies, efforts are being made to discover small molecule inhibitors of DNA glycosylases that may be used as potential drugs in cancer therapy.
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28
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Wong JR, Shao F. Hole Transport in A-form DNA/RNA Hybrid Duplexes. Sci Rep 2017; 7:40293. [PMID: 28084308 PMCID: PMC5233965 DOI: 10.1038/srep40293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/01/2016] [Indexed: 01/28/2023] Open
Abstract
DNA/RNA hybrid duplexes are prevalent in many cellular functions and are an attractive target form for electrochemical biosensing and electric nanodevice. However the electronic conductivities of DNA/RNA hybrid duplex remain relatively unexplored and limited further technological applications. Here cyclopropyl-modified deoxyribose- and ribose-adenosines were developed to explore hole transport (HT) in both DNA duplex and DNA/RNA hybrids by probing the transient hole occupancies on adenine tracts. HT yields through both B-form and A-form double helixes displayed similar shallow distance dependence, although the HT yields of DNA/RNA hybrid duplexes were lower than those of DNA duplexes. The lack of oscillatory periods and direction dependence in HT through both helixes implied efficient hole propagation can be achieved via the hole delocalization and coherent HT over adenine tracts, regardless of the structural variations.
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Affiliation(s)
- Jiun Ru Wong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)
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29
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Stiban J, So M, Kaguni LS. Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor. BIOCHEMISTRY (MOSCOW) 2017; 81:1066-1080. [PMID: 27908232 DOI: 10.1134/s0006297916100059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis. Whereas the identification of iron-sulfur containing proteins and their roles in numerous aspects of cellular function has been a long-standing research area, that in mitochondria is comparatively recent, and it is likely that their roles within mitochondria have been only partially revealed. We review the status of the field and provide examples of other cellular iron-sulfur proteins to highlight their multifarious roles.
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Affiliation(s)
- Johnny Stiban
- Birzeit University, Department of Biology and Biochemistry, West Bank Birzeit, 627, Palestine.
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30
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Koley Seth B, Saha A, Haldar S, Chakraborty PP, Saha P, Basu S. Structure dependent selective efficacy of pyridine and pyrrole based Cu(II) Schiff base complexes towards in vitro cytotoxicity, apoptosis and DNA-bases binding in ground and excited state. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:463-472. [DOI: 10.1016/j.jphotobiol.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 11/29/2022]
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31
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Synthesis, crystal structure and electronic properties of [3.3]metaparacyclophane-bridged bimetallic ruthenium alkynyl complexes. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2015.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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32
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Li Y, Artés JM, Hihath J. Long-Range Charge Transport in Adenine-Stacked RNA:DNA Hybrids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:432-7. [PMID: 26596516 DOI: 10.1002/smll.201502399] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/07/2015] [Indexed: 05/05/2023]
Abstract
An extremely important biological component, RNA:DNA can also be used to design nanoscale structures such as molecular wires. The conductance of single adenine-stacked RNA:DNA hybrids is rapidly and reproducibly measured using the break junction approach. The conductance decreases slightly over a large range of molecular lengths, suggesting that RNA:DNA can be used as an oligonucleotide wire.
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Affiliation(s)
- Yuanhui Li
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, 95616, USA
| | - Juan M Artés
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, 95616, USA
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, 95616, USA
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33
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Chen L, Chao H, Zhao Q, Zheng X, Li H. Photoluminescence quenching of [Ru(bpy)2(atatp)]2+ bound to a condensed DNA matrix. J Inorg Biochem 2016; 154:1-6. [DOI: 10.1016/j.jinorgbio.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 09/24/2015] [Accepted: 10/05/2015] [Indexed: 12/25/2022]
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34
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Nano-porous network of DMTD-Ag coordination polymer for the ultra trace detection of anticholinergic drug. POLYMER 2016. [DOI: 10.1016/j.polymer.2015.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Ruthenium(II) bipyridine complexes with pendant anthracenyl and naphthyl moieties: A strategy for a ROS generator with DNA binding selectivity. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.09.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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36
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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37
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Magliulo M, Manoli K, Macchia E, Palazzo G, Torsi L. Tailoring Functional Interlayers in Organic Field-Effect Transistor Biosensors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:7528-51. [PMID: 25429859 DOI: 10.1002/adma.201403477] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/24/2014] [Indexed: 05/18/2023]
Abstract
This review aims to provide an update on the development involving dielectric/organic semiconductor (OSC) interfaces for the realization of biofunctional organic field-effect transistors (OFETs). Specific focus is given on biointerfaces and recent technological approaches where biological materials serve as interlayers in back-gated OFETs for biosensing applications. Initially, to better understand the effects produced by the presence of biomolecules deposited at the dielectric/OSC interfacial region, the tuning of the dielectric surface properties by means of self-assembled monolayers is discussed. Afterward, emphasis is given to the modification of solid-state dielectric surfaces, in particular inorganic dielectrics, with biological molecules such as peptides and proteins. Special attention is paid on how the presence of an interlayer of biomolecules and bioreceptors underneath the OSC impacts on the charge transport and sensing performance of the device. Moreover, naturally occurring materials, such as carbohydrates and DNA, used directly as bulk gating materials in OFETs are reviewed. The role of metal contact/OSC interface in the overall performance of OFET-based sensors is also discussed.
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Affiliation(s)
- Maria Magliulo
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
| | - Kyriaki Manoli
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
| | - Eleonora Macchia
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
- Dipartimento Interateneo di Fisica "M. Merlin", Università degli Studi di Bari "A. Moro", Via Orabona, 470125, Bari, Italy
| | - Gerardo Palazzo
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
| | - Luisa Torsi
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
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38
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Pluhařová E, Slavíček P, Jungwirth P. Modeling photoionization of aqueous DNA and its components. Acc Chem Res 2015; 48:1209-17. [PMID: 25738773 DOI: 10.1021/ar500366z] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Radiation damage to DNA is usually considered in terms of UVA and UVB radiation. These ultraviolet rays, which are part of the solar spectrum, can indeed cause chemical lesions in DNA, triggered by photoexcitation particularly in the UVB range. Damage can, however, be also caused by higher energy radiation, which can ionize directly the DNA or its immediate surroundings, leading to indirect damage. Thanks to absorption in the atmosphere, the intensity of such ionizing radiation is negligible in the solar spectrum at the surface of Earth. Nevertheless, such an ionizing scenario can become dangerously plausible for astronauts or flight personnel, as well as for persons present at nuclear power plant accidents. On the beneficial side, ionizing radiation is employed as means for destroying the DNA of cancer cells during radiation therapy. Quantitative information about ionization of DNA and its components is important not only for DNA radiation damage, but also for understanding redox properties of DNA in redox sensing or labeling, as well as charge migration along the double helix in nanoelectronics applications. Until recently, the vast majority of experimental and computational data on DNA ionization was pertinent to its components in the gas phase, which is far from its native aqueous environment. The situation has, however, changed for the better due to the advent of photoelectron spectroscopy in liquid microjets and its most recent application to photoionization of aqueous nucleosides, nucleotides, and larger DNA fragments. Here, we present a consistent and efficient computational methodology, which allows to accurately evaluate ionization energies and model photoelectron spectra of aqueous DNA and its individual components. After careful benchmarking, the method based on density functional theory and its time-dependent variant with properly chosen hybrid functionals and polarizable continuum solvent model provides ionization energies with accuracy of 0.2-0.3 eV, allowing for faithful modeling and interpretation of DNA photoionization. The key finding is that the aqueous medium is remarkably efficient in screening the interactions within DNA such that, unlike in the gas phase, ionization of a base, nucleoside, or nucleotide depends only very weakly on the particular DNA context. An exception is the electronic interaction between neighboring bases which can lead to sequence-specific effects, such as a partial delocalization of the cationic hole upon ionization enabled by presence of adjacent bases of the same type.
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Affiliation(s)
- Eva Pluhařová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Petr Slavíček
- University of Chemistry and Technology, Department
of Physical Chemistry, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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39
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Wong JR, Lee KJ, Shu JJ, Shao F. Magnetic Fields Facilitate DNA-Mediated Charge Transport. Biochemistry 2015; 54:3392-9. [DOI: 10.1021/acs.biochem.5b00295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiun Ru Wong
- Division
of Chemistry and Biological Chemistry, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Kee Jin Lee
- School of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Jian-Jun Shu
- School of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Fangwei Shao
- Division
of Chemistry and Biological Chemistry, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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40
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Zaffino RL, Galan T, Pardo WA, Mir M, Samitier J. Nanoprobes for enhanced electrochemical DNA sensors. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 7:817-27. [DOI: 10.1002/wnan.1344] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/07/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Rosa Letizia Zaffino
- Nanobioengineering Laboratory; Institute for Bioengineering of Catalonia (IBEC); Barcelona Spain
- Department of Electronics; Barcelona University (UB); Barcelona Spain
| | - Teresa Galan
- Nanobioengineering Laboratory; Institute for Bioengineering of Catalonia (IBEC); Barcelona Spain
- Department of Electronics; Barcelona University (UB); Barcelona Spain
| | - Wilmer Alfonso Pardo
- Nanobioengineering Laboratory; Institute for Bioengineering of Catalonia (IBEC); Barcelona Spain
- Department of Electronics; Barcelona University (UB); Barcelona Spain
| | - Mònica Mir
- Nanobioengineering Laboratory; Institute for Bioengineering of Catalonia (IBEC); Barcelona Spain
- Centro de Investigación Biomédica en Red de Bioingeniería; Biomateriales y Nanomedicina (CIBER-BBN); Zaragoza Spain
| | - Josep Samitier
- Nanobioengineering Laboratory; Institute for Bioengineering of Catalonia (IBEC); Barcelona Spain
- Department of Electronics; Barcelona University (UB); Barcelona Spain
- Centro de Investigación Biomédica en Red de Bioingeniería; Biomateriales y Nanomedicina (CIBER-BBN); Zaragoza Spain
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41
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Narth C, Gillet N, Cailliez F, Lévy B, de la Lande A. Electron transfer, decoherence, and protein dynamics: insights from atomistic simulations. Acc Chem Res 2015; 48:1090-7. [PMID: 25730126 DOI: 10.1021/ar5002796] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron transfer in biological systems drives the processes of life. From cellular respiration to photosynthesis and enzymatic catalysis, electron transfers (ET) are chemical processes on which essential biological functions rely. Over the last 40 years, scientists have sought understanding of how these essential processes function in biology. One important breakthrough was the discovery that Marcus theory (MT) of electron transfer is applicable to biological systems. Chemists have experimentally collected both the reorganization energies (λ) and the driving forces (ΔG°), two parameters of Marcus theory, for a large variety of ET processes in proteins. At the same time, theoretical chemists have developed computational approaches that rely on molecular dynamics and quantum chemistry calculations to access numerical estimates of λ and ΔG°. Yet another crucial piece in determining the rate of an electron transfer is the electronic coupling between the initial and final electronic wave functions. This is an important prefactor in the nonadiabatic rate expression, since it reflects the probability that an electron tunnels from the electron donor to the acceptor through the intervening medium. The fact that a protein matrix supports electron tunneling much more efficiently than vacuum is now well documented, both experimentally and theoretically. Meanwhile, many chemists have provided examples of the rich physical chemistry that can be induced by protein dynamics. This Account describes our studies of the dynamical effects on electron tunneling. We present our analysis of two examples of natural biological systems through MD simulations and tunneling pathway analyses. Through these examples, we show that protein dynamics sustain efficient tunneling. Second, we introduce two time scales: τcoh and τFC. The former characterizes how fast the electronic coupling varies with nuclear vibrations (which cause dephasing). The latter reflects the time taken by the system to leave the crossing region. In the framework of open quantum systems, τFC is a short time approximation of the characteristic decoherence time of the electronic subsystem in interaction with its nuclear environment. The comparison of the respective values of τcoh and τFC allows us to probe the occurrence of non-Condon effects. We use ab initio MD simulations to analyze how decoherence appears in several biological cofactors. We conclude that we cannot account for its order of magnitude by considering only the atoms or bonds directly concerned with the transfer. Decoherence results from contributions from all atoms of the system appearing with a time delay that increases with the distance from the primarily concerned atoms or bonds. The delay and magnitude of the contributions depend on the chemical nature of the system. Finally, we present recent developments based on constrained DFT for efficient and accurate evaluations of the electronic coupling in ab initio MD simulations. These are promising methods to study the subtle fluctuations of the electronic coupling and the mechanisms of electronic decoherence in biological systems.
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Affiliation(s)
- Christophe Narth
- Laboratoire
de Chimie Théorique, CNRS UMR 7616, Université Pierre et Marie Curie, case courrier 137. 4, Place Jussieu, 75252 Cedex 05 Paris, France
| | - Natacha Gillet
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Fabien Cailliez
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Bernard Lévy
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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43
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Schaefer K, Geil WM, Sweredoski MJ, Moradian A, Hess S, Barton JK. Oxidation of p53 through DNA charge transport involves a network of disulfides within the DNA-binding domain. Biochemistry 2015; 54:932-41. [PMID: 25584637 PMCID: PMC4310631 DOI: 10.1021/bi501424v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/19/2014] [Indexed: 11/29/2022]
Abstract
Transcription factor p53 plays a critical role in the cellular response to stress stimuli. We have seen that p53 dissociates selectively from various promoter sites as a result of oxidation at long-range through DNA-mediated charge transport (CT). Here, we examine this chemical oxidation and determine the residues in p53 that are essential for oxidative dissociation, focusing on the network of cysteine residues adjacent to the DNA-binding site. Of the eight mutants studied, only the C275S mutation shows decreased affinity for the Gadd45 promoter site. However, both mutations C275S and C277S result in substantial attenuation of oxidative dissociation, with C275S causing the most severe attenuation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide-labeled, whereas oxidized cysteines participating in disulfide bonds were (13)C2D2-iodoacetamide-labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed by mass spectrometry. A distinct shift in peptide labeling toward (13)C2D2-iodoacetamide-labeled cysteines is observed in oxidized samples, confirming that chemical oxidation of p53 occurs at long range. All observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds among the cysteine network. On the basis of these data, it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA.
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Affiliation(s)
- Kathryn
N. Schaefer
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Wendy M. Geil
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Michael J. Sweredoski
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Annie Moradian
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Sonja Hess
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
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Abstract
The unique characteristics of DNA charge transport (CT) have prompted an examination of roles for this chemistry within a biological context. Not only can DNA CT facilitate long-range oxidative damage of DNA, but redox-active proteins can couple to the DNA base stack and participate in long-range redox reactions using DNA CT. DNA transcription factors with redox-active moieties such as SoxR and p53 can use DNA CT as a form of redox sensing. DNA CT chemistry also provides a means to monitor the integrity of the DNA, given the sensitivity of DNA CT to perturbations in base stacking as arise with mismatches and lesions. Enzymes that utilize this chemistry include an interesting and ever-growing class of DNA-processing enzymes involved in DNA repair, replication, and transcription that have been found to contain 4Fe-4S clusters. DNA repair enzymes containing 4Fe-4S clusters, that include endonuclease III (EndoIII), MutY, and DinG from bacteria, as well as XPD from archaea, have been shown to be redox-active when bound to DNA, share a DNA-bound redox potential, and can be reduced and oxidized at long-range via DNA CT. Interactions between DNA and these proteins in solution, in addition to genetics experiments within Escherichia coli, suggest that DNA-mediated CT can be used as a means of cooperative signaling among DNA repair proteins that contain 4Fe-4S clusters as a first step in finding DNA damage, even within cells. On the basis of these data, we can consider also how DNA-mediated CT may be used as a means of signaling to coordinate DNA processing across the genome.
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Affiliation(s)
- Michael A Grodick
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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45
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Xu E, Lv Y, Liu J, Gu X, Zhang S. An electrochemical study based on thymine–Hg–thymine DNA base pair mediated charge transfer processes. RSC Adv 2015. [DOI: 10.1039/c5ra06238a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The (TT)n might have more π-overlapping than the corresponding matched base pairs, and the intercalation of Hg(ii) into TT may further increase this overlapping, causing faster CT kinetics.
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Affiliation(s)
- Ensheng Xu
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Yanqin Lv
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Jifeng Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
- Key Laboratory of Food Nutrition and Safety
| | - Xiaohong Gu
- Shandong Provincial Key Lab of Test Technology on Food Quality and Safety
- Shandong Academy of Agricultural Sciences
- Jinan 250100
- China
| | - Shuqiu Zhang
- Shandong Provincial Key Lab of Test Technology on Food Quality and Safety
- Shandong Academy of Agricultural Sciences
- Jinan 250100
- China
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46
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Astakhova TY, Kashin VA, Likhachev VN, Vinogradov GA. Exact solution for polarons on the anharmonic lattice and charge transfer in biopolymers. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414110028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sales MO, de Moura FABF. Electron-soliton dynamics in chains with cubic nonlinearity. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:415401. [PMID: 25244998 DOI: 10.1088/0953-8984/26/41/415401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In our work, we consider the problem of electronic transport mediated by coupling with solitonic elastic waves. We study the electronic transport in a 1D unharmonic lattice with a cubic interaction between nearest neighboring sites. The electron-lattice interaction was considered as a linear function of the distance between neighboring atoms in our study. We numerically solve the dynamics equations for the electron and lattice and compute the dynamics of an initially localized electronic wave-packet. Our results suggest that the solitonic waves that exist within this nonlinear lattice can control the electron dynamics along the chain. Moreover, we demonstrate that the existence of a mobile electron-soliton pair exhibits a counter-intuitive dependence with the value of the electron-lattice coupling.
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Affiliation(s)
- M O Sales
- Instituto de Física, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
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de Oliveira AHS, da Silva AE, de Oliveira IM, Henriques JAP, Agnez-Lima LF. MutY-glycosylase: an overview on mutagenesis and activities beyond the GO system. Mutat Res 2014; 769:119-31. [PMID: 25771731 DOI: 10.1016/j.mrfmmm.2014.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/28/2014] [Accepted: 08/04/2014] [Indexed: 02/06/2023]
Abstract
MutY is a glycosylase known for its role in DNA base excision repair (BER). It is critically important in the prevention of DNA mutations derived from 7,8-dihydro-8-oxoguanine (8-oxoG), which are the major lesions resulting from guanine oxidation. MutY has been described as a DNA repair enzyme in the GO system responsible for removing adenine residues misincorporated in 8-oxoG:A mispairs, avoiding G:C to T:A mutations. Further studies have shown that this enzyme binds to other mispairs, interacts with several enzymes, avoids different transversions/transitions in DNA, and is involved in different repair pathways. Additional activities have been reported for MutY, such as the repair of replication errors in newly synthesized DNA strands through its glycosylase activity. Moreover, MutY is a highly conserved enzyme present in several prokaryotic and eukaryotic organisms. MutY defects are associated with a hereditary colorectal cancer syndrome termed MUTYH-associated polyposis (MAP). Here, we have reviewed the roles of MutY in the repair of mispaired bases in DNA as well as its activities beyond the GO system.
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Affiliation(s)
- Ana Helena Sales de Oliveira
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Departamento de Biofísica e Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Acarízia Eduardo da Silva
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Iuri Marques de Oliveira
- Departamento de Biofísica e Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - João Antônio Pegas Henriques
- Departamento de Biofísica e Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto de Biotecnologia, Departamento de Ciências Biomédicas, Universidade de Caxias do Sul (UCS), Caxias do Sul, RS, Brazil
| | - Lucymara Fassarella Agnez-Lima
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil.
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Abstract
Transcription factor p53 is the most commonly altered gene in human cancer. As a redox-active protein in direct contact with DNA, p53 can directly sense oxidative stress through DNA-mediated charge transport. Electron hole transport occurs over long distances through the π-stacked bases and leads to the oxidative dissociation of p53. The extent of protein dissociation depends upon the redox potential of the DNA in direct contact with each p53 monomer. The DNA sequence dependence of p53 oxidative dissociation was examined by electrophoretic mobility shift assays using oligonucleotides containing both synthetic and human p53 consensus sequences with an appended photooxidant, anthraquinone. Greater p53 dissociation is observed from sequences containing low-redox potential purine regions, particularly guanine triplets. Using denaturing polyacrylamide gel electrophoresis of irradiated anthraquinone-modified DNA, the DNA damage sites corresponding to sites of preferred electron hole localization were determined. The resulting DNA damage preferentially localizes to guanine doublets and triplets. Oxidative DNA damage is inhibited in the presence of p53, but only at sites in direct contact with p53. From these data, predictions about the sensitivity of human p53-binding sites to oxidative stress as well as possible biological implications have been made. On the basis of our data, the guanine pattern within the purine region of each p53-binding site determines the response of p53 to DNA oxidation, yielding for some sequences the oxidative dissociation of p53 from a distance and thereby providing another potential role for DNA charge transport chemistry within the cell.
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Affiliation(s)
- Kathryn N Schaefer
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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