1
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He Z, Wang Z, Lu L, Wang X, Guo G. Enhanced recognition of G-quadruplex DNA oxidative damage based on DNA-mediated charge transfer. Bioelectrochemistry 2024; 158:108714. [PMID: 38653106 DOI: 10.1016/j.bioelechem.2024.108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/25/2024]
Abstract
G-quadruplex (G4) DNA is present in human telomere oligonucleotide sequences. Oxidative damage to telomeric DNA accelerates telomere shortening, which is strongly associated with aging and cancer. Most of the current analyses on oxidative DNA damage are based on ds-DNA. Here, we developed a electrochemiluminescence (ECL) probe for enhanced recognition of oxidative damage in G4-DNA based on DNA-mediated charge transfer (CT), which could specifically recognize damaged sites depending on the position of 8-oxoguanine (8-oxoG). First, a uniform G4-DNA monolayer interface was fabricated; the G4-DNA mediated CT properties were examined using an iridium(III) complex [Ir(ppy)2(pip)]PF6 stacked with G4-DNA as an indicator. The results showed that G4-DNA with 8-oxoG attenuated DNA CT. The topological effects of oxidative damage at different sites of G4-DNA and their effects on DNA CT were revealed. The sensing platform was also used for the sensitive and quantitative detection of 8-oxoG in G4-DNA, with a detection limit of 28.9 fmol. Overall, these findings present a sensitive platform to study G4-DNA structural and stability changes caused by oxidative damage as well as the specific and quantitative detection of oxidation sites. The different damage sites in the G-quadruplex could provide detailed clues for understanding the function of G4-associated telomere functional enzymes.
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Affiliation(s)
- Zhangjin He
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Ziqi Wang
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China; Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China.
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
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2
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Velasquez N, B Nunes F, Travnikova O, Ismail I, Guillemin R, Martins JB, Céolin D, Journel L, Fillaud L, Koulentianos D, Kamal C, Püttner R, Piancastelli MN, Simon M, Odelius M, Iannuzzi M, Marchenko T. X-ray induced ultrafast charge transfer in thiophene-based conjugated polymers controlled by core-hole clock spectroscopy. Phys Chem Chem Phys 2024; 26:1234-1244. [PMID: 38099819 DOI: 10.1039/d3cp04303g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
We explore ultrafast charge transfer (CT) resonantly induced by hard X-ray radiation in organic thiophene-based polymers at the sulfur K-edge. A combination of core-hole clock spectroscopy with real-time propagation time-dependent density functional theory simulations gives an insight into the electron dynamics underlying the CT process. Our method provides control over CT by a selective excitation of a specific resonance in the sulfur atom with monochromatic X-ray radiation. Our combined experimental and theoretical investigation establishes that the dominant mechanism of CT in polymer powders and films consists of electron delocalisation along the polymer chain occurring on the low-femtosecond time scale.
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Affiliation(s)
- Nicolas Velasquez
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
| | - Fernanda B Nunes
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland.
| | - Oksana Travnikova
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Iyas Ismail
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Renaud Guillemin
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Jessica B Martins
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
| | - Denis Céolin
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Loïc Journel
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Laure Fillaud
- Sorbonne Université, CNRS, Laboratoire Interfaces et Systèmes Electrochimiques, LISE, F-75005 Paris Cedex 05, France
| | - Dimitris Koulentianos
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Gothenburg, Sweden
| | - Chinnathambi Kamal
- Theory and Simulations Laboratory, TCPS, Raja Ramanna Centre for Advanced Technology, Indore 452013, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Ralph Püttner
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Maria Novella Piancastelli
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
| | - Marc Simon
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
| | - Michael Odelius
- Department of Physics, Stockholm University, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland.
| | - Tatiana Marchenko
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, F-75005 Paris Cedex 05, France.
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette, France
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3
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Masi A, Capobianco A, Bobrowski K, Peluso A, Chatgilialoglu C. Hydroxyl Radical vs. One-Electron Oxidation Reactivities in an Alternating GC Double-Stranded Oligonucleotide: A New Type Electron Hole Stabilization. Biomolecules 2023; 13:1493. [PMID: 37892175 PMCID: PMC10605094 DOI: 10.3390/biom13101493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
We examined the reaction of hydroxyl radicals (HO•) and sulfate radical anions (SO4•-), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO• to the G:C pair moiety, affording the [8-HO-G:C]• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H+):C]• after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.
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Affiliation(s)
- Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
- Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
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4
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Siebert R, Ammerpohl O, Rossini M, Herb D, Rau S, Plenio MB, Jelezko F, Ankerhold J. A quantum physics layer of epigenetics: a hypothesis deduced from charge transfer and chirality-induced spin selectivity of DNA. Clin Epigenetics 2023; 15:145. [PMID: 37684676 PMCID: PMC10492394 DOI: 10.1186/s13148-023-01560-3] [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: 06/09/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Epigenetic mechanisms are informational cellular processes instructing normal and diseased phenotypes. They are associated with DNA but without altering the DNA sequence. Whereas chemical processes like DNA methylation or histone modifications are well-accepted epigenetic mechanisms, we herein propose the existence of an additional quantum physics layer of epigenetics. RESULTS We base our hypothesis on theoretical and experimental studies showing quantum phenomena to be active in double-stranded DNA, even under ambient conditions. These phenomena include coherent charge transfer along overlapping pi-orbitals of DNA bases and chirality-induced spin selectivity. Charge transfer via quantum tunneling mediated by overlapping orbitals results in charge delocalization along several neighboring bases, which can even be extended by classical (non-quantum) electron hopping. Such charge transfer is interrupted by flipping base(s) out of the double-strand e.g., by DNA modifying enzymes. Charge delocalization can directly alter DNA recognition by proteins or indirectly by DNA structural changes e.g., kinking. Regarding sequence dependency, charge localization, shown to favor guanines, could influence or even direct epigenetic changes, e.g., modification of cytosines in CpG dinucleotides. Chirality-induced spin selectivity filters electrons for their spin along DNA and, thus, is not only an indicator for quantum coherence but can potentially affect DNA binding properties. CONCLUSIONS Quantum effects in DNA are prone to triggering and manipulation by external means. By the hypothesis put forward here, we would like to foster research on "Quantum Epigenetics" at the interface of medicine, biology, biochemistry, and physics to investigate the potential epigenetic impact of quantum physical principles on (human) life.
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Affiliation(s)
- Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany.
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Mirko Rossini
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
| | - Dennis Herb
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
| | - Sven Rau
- Institute of Inorganic Chemistry I, Ulm University, 89081, Ulm, Germany
| | - Martin B Plenio
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute of Theoretical Physics, Ulm University, 89081, Ulm, Germany
| | - Fedor Jelezko
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Quantum Optics, Ulm University, 89081, Ulm, Germany
| | - Joachim Ankerhold
- Center for Integrated Quantum Science and Technology (IQST) Ulm-Stuttgart, Ulm, Germany
- Institute for Complex Quantum Systems, Ulm University, 89069, Ulm, Germany
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5
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Filippidou MK, Kanaris AI, Aslanidis E, Rapesi A, Tsounidi D, Ntouskas S, Skotadis E, Tsekenis G, Tsoukalas D, Tserepi A, Chatzandroulis S. Integrated Plastic Microfluidic Device for Heavy Metal Ion Detection. MICROMACHINES 2023; 14:1595. [PMID: 37630131 PMCID: PMC10456536 DOI: 10.3390/mi14081595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
The presence of heavy metal ions in soil, air and water constitutes an important global environmental threat, as these ions accumulate throughout the food chain, contributing to the rise of chronic diseases, including, amongst others, cancer and kidney failure. To date, many efforts have been made for their detection, but there is still a need for the development of sensitive, low-cost, and portable devices able to conduct on-site detection of heavy metal ions. In this work, we combine microfluidic technology and electrochemical sensing in a plastic chip for the selective detection of heavy metal ions utilizing DNAzymes immobilized in between platinum nanoparticles (PtNPs), demonstrating a reliable portable solution for water pollution monitoring. For the realization of the microfluidic-based heavy metal ion detection device, a fast and easy-to-implement fabrication method based on the photolithography of dry photosensitive layers is proposed. As a proof of concept, we demonstrate the detection of Pb2+ ions using the prototype microfluidic device.
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Affiliation(s)
- Myrto Kyriaki Filippidou
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Aris Ioannis Kanaris
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Evangelos Aslanidis
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
| | - Annita Rapesi
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece (G.T.)
| | - Dimitra Tsounidi
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece (G.T.)
| | - Sotirios Ntouskas
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Evangelos Skotadis
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
| | - George Tsekenis
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece (G.T.)
| | - Dimitris Tsoukalas
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
| | - Angeliki Tserepi
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Stavros Chatzandroulis
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
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6
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Mantela M, Lambropoulos K, Simserides C. Charge transport properties of ideal and natural DNA segments, as mutation detectors. Phys Chem Chem Phys 2023; 25:7750-7762. [PMID: 36857625 DOI: 10.1039/d3cp00268c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors. Ideal means textbook geometry. Natural means naturally distorted sequences; geometry taken from available databases. A tight-binding (TB) wire model at the base-pair level is recruited, together with a transfer matrix technique. The relevant TB parameters are obtained using a linear combination of all valence orbitals of all atoms, using geometry, either ideal or natural, as the only input. The investigated DNA sequences contain: (i) point substitution mutations - specifically, the transitions guanine (G) ↔ adenine (A) - and (ii) sequences extracted from human chromosomes, modified by expanding the cytosine-adenine-guanine triplet [(CAG)n repeats] to mimic the following diseases: (a) Huntington's disease, (b) Kennedy's disease, (c) Spinocerebellar ataxia 6, (d) Spinocerebellar ataxia 7. Quantities such as eigenspectra, density of states, transmission coefficients, and the - more experimentally relevant - current-voltage (I-V) curves are studied, intending to find adequate features to recognize mutations. To this end, the normalised deviation of the I-V curve from the origin (NDIV) is also defined. The features of the NDIV seem to provide a clearer picture, being sensitive to the number of point mutations and allowing to characterise the degree of danger of developing the aforementioned diseases.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
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7
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Rooman M, Pucci F. Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules. J Chem Inf Model 2023; 63:1766-1775. [PMID: 36877828 DOI: 10.1021/acs.jcim.2c01525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The electronic properties of DNA molecules, defined by the sequence-dependent ionization potentials of nucleobases, enable long-range charge transport along the DNA stacks. This has been linked to a range of key physiological processes in the cells and to the triggering of nucleobase substitutions, some of which may cause diseases. To gain molecular-level understanding of the sequence dependence of these phenomena, we estimated the vertical ionization potential (vIP) of all possible nucleobase stacks in B-conformation, containing one to four Gua, Ade, Thy, Cyt, or methylated Cyt. To do this, we used quantum chemistry calculations and more precisely the second-order Møller-Plesset perturbation theory (MP2) and three double-hybrid density functional theory methods, combined with several basis sets for describing atomic orbitals. The calculated vIP of single nucleobases were compared to experimental data and those of nucleobase pairs, triplets, and quadruplets, to observed mutability frequencies in the human genome, reported to be correlated with vIP values. This comparison selected MP2 with the 6-31G* basis set as the best of the tested calculation levels. These results were exploited to set up a recursive model, called vIPer, which estimates the vIP of all possible single-stranded DNA sequences of any length based on the calculated vIPs of overlapping quadruplets. vIPer's vIP values correlate well with oxidation potentials measured by cyclic voltammetry and activities obtained through photoinduced DNA cleavage experiments, further validating our approach. vIPer is freely available on the github.com/3BioCompBio/vIPer repository.
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Affiliation(s)
- Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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8
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Abstract
The number of (TTAGGG)n repeats at the ends of chromosomes is highly variable between individual chromosomes, between different cells and between species. Progressive loss of telomere repeats limits the proliferation of pre-malignant human cells but also contributes to aging by inducing apoptosis and senescence in normal cells. Despite enormous progress in understanding distinct pathways that result in loss and gain of telomeric DNA in different cell types, many questions remain. Further studies are needed to delineate the role of damage to telomeric DNA, replication errors, chromatin structure, liquid-liquid phase transition, telomeric transcripts (TERRA) and secondary DNA structures such as guanine quadruplex structures, R-loops and T-loops in inducing gains and losses of telomere repeats in different cell types. Limitations of current telomere length measurements techniques and differences in telomere biology between species and different cell types complicate generalizations about the role of telomeres in aging and cancer. Here some of the factors regulating the telomere length in embryonic and adult cells in mammals are discussed from a mechanistic and evolutionary perspective.
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Affiliation(s)
- Peter Lansdorp
- Terry Fox Laboratory, British Columbia (BC) Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Peter Lansdorp,
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9
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Suzuki S, Homma A, Nishi R, Mizuno H, Kawauchi S, Fukuhara G. A Dynamically Responsive Chemosensor That Can be Modulated by an Effector: Amplification Sensing by Positive Heterotropic Allosterism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sho Suzuki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Amane Homma
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Reiya Nishi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Susumu Kawauchi
- Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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10
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Bi X, Miao K, Wei L. Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen-Deuterium Exchange. J Am Chem Soc 2022; 144:8504-8514. [PMID: 35508077 DOI: 10.1021/jacs.2c01991] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen-deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm-1, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pKas and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.
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Affiliation(s)
- Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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11
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Kogikoski S, Dutta A, Bald I. Spatial Separation of Plasmonic Hot-Electron Generation and a Hydrodehalogenation Reaction Center Using a DNA Wire. ACS NANO 2021; 15:20562-20573. [PMID: 34875168 PMCID: PMC8717627 DOI: 10.1021/acsnano.1c09176] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Using hot charge carriers far from a plasmonic nanoparticle surface is very attractive for many applications in catalysis and nanomedicine and will lead to a better understanding of plasmon-induced processes, such as hot-charge-carrier- or heat-driven chemical reactions. Herein we show that DNA is able to transfer hot electrons generated by a silver nanoparticle over several nanometers to drive a chemical reaction in a molecule nonadsorbed on the surface. For this we use 8-bromo-adenosine introduced in different positions within a double-stranded DNA oligonucleotide. The DNA is also used to assemble the nanoparticles into nanoparticles ensembles enabling the use of surface-enhanced Raman scattering to track the decomposition reaction. To prove the DNA-mediated transfer, the probe molecule was insulated from the source of charge carriers, which hindered the reaction. The results indicate that DNA can be used to study the transfer of hot electrons and the mechanisms of advanced plasmonic catalysts.
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Affiliation(s)
- Sergio Kogikoski
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
- Department
of Analytical Chemistry, Institute of Chemistry, State University of Campinas (UNICAMP), P.O. Box 6154, 13083-970, Campinas São Paulo, Brazil
| | - Anushree Dutta
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Ilko Bald
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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12
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Gupta N, Wilkinson EA, Karuppannan SK, Bailey L, Vilan A, Zhang Z, Qi DC, Tadich A, Tuite EM, Pike AR, Tucker JHR, Nijhuis CA. Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions. J Am Chem Soc 2021; 143:20309-20319. [PMID: 34826219 PMCID: PMC8662729 DOI: 10.1021/jacs.1c09549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 11/29/2022]
Abstract
Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.
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Affiliation(s)
- Nipun
Kumar Gupta
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
| | - Edward A. Wilkinson
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Senthil Kumar Karuppannan
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Lily Bailey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Ayelet Vilan
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Ziyu Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Dong-Chen Qi
- Centre
for Materials Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Anton Tadich
- Australian
Synchrotron Clayton, 800 Blackburn Rd, Clayton, Victoria 3168, Australia
| | - Eimer M. Tuite
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Andrew R. Pike
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Christian A. Nijhuis
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science and Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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13
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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14
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Pinto MN, Ter Beek J, Ekanger LA, Johansson E, Barton JK. The [4Fe4S] Cluster of Yeast DNA Polymerase ε Is Redox Active and Can Undergo DNA-Mediated Signaling. J Am Chem Soc 2021; 143:16147-16153. [PMID: 34559527 PMCID: PMC8499023 DOI: 10.1021/jacs.1c07150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many DNA replication and DNA repair enzymes have been found to carry [4Fe4S] clusters. The major leading strand polymerase, DNA polymerase ε (Pol ε) from Saccharomyces cerevisiae, was recently reported to have a [4Fe4S] cluster located within the catalytic domain of the largest subunit, Pol2. Here the redox characteristics of the [4Fe4S] cluster in the context of that domain, Pol2CORE, are explored using DNA electrochemistry, and the effects of oxidation and rereduction on polymerase activity are examined. The exonuclease deficient variant D290A/E292A, Pol2COREexo-, was used to limit DNA degradation. While no redox signal is apparent for Pol2COREexo- on DNA-modified electrodes, a large cathodic signal centered at -140 mV vs NHE is observed after bulk oxidation. A double cysteine to serine mutant (C665S/C668S) of Pol2COREexo-, which lacks the [4Fe4S] cluster, shows no similar redox signal upon oxidation. Significantly, protein oxidation yields a sharp decrease in polymerization, while rereduction restores activity almost to the level of untreated enzyme. Moreover, the addition of reduced EndoIII, a bacterial DNA repair enzyme containing [4Fe4S]2+, to oxidized Pol2COREexo- bound to its DNA substrate also significantly restores polymerase activity. In contrast, parallel experiments with EndoIIIY82A, a variant of EndoIII, defective in DNA charge transport (CT), does not show restoration of activity of Pol2COREexo-. We propose a model in which EndoIII bound to the DNA duplex may shuttle electrons through DNA to the DNA-bound oxidized Pol2COREexo- via DNA CT and that this DNA CT signaling offers a means to modulate the redox state and replication by Pol ε.
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Affiliation(s)
- Miguel N Pinto
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-910 87 Umeå, Sweden
| | - Levi A Ekanger
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.,Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-910 87 Umeå, Sweden
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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15
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The Two Faces of the Guanyl Radical: Molecular Context and Behavior. Molecules 2021; 26:molecules26123511. [PMID: 34207639 PMCID: PMC8227002 DOI: 10.3390/molecules26123511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.
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16
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Man Ngo F, Tse ECM. Bioinorganic Platforms for Sensing, Biomimicry, and Energy Catalysis. CHEM LETT 2021. [DOI: 10.1246/cl.200875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fung Man Ngo
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, University of Hong Kong, Hong Kong SAR, P. R. China
- Advanced Functional Materials Laboratory, HKU Zhejiang Institute of Research and Innovation, Zhejiang 311305, P. R. China
| | - Edmund C. M. Tse
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, University of Hong Kong, Hong Kong SAR, P. R. China
- Advanced Functional Materials Laboratory, HKU Zhejiang Institute of Research and Innovation, Zhejiang 311305, P. R. China
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17
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Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons. Symmetry (Basel) 2021. [DOI: 10.3390/sym13020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.
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18
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Mateus P, Jacquet A, Méndez-Ardoy A, Boulloy A, Kauffmann B, Pecastaings G, Buffeteau T, Ferrand Y, Bassani DM, Huc I. Sensing a binding event through charge transport variations using an aromatic oligoamide capsule. Chem Sci 2021; 12:3743-3750. [PMID: 34163648 PMCID: PMC8179446 DOI: 10.1039/d0sc06060g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/21/2021] [Indexed: 12/31/2022] Open
Abstract
The selective binding properties of a 13-mer oligoamide foldamer capsule composed of 4 different aromatic subunits are reported. The capsule was designed to recognize dicarboxylic acids through multiple-point interactions owing to a combination of protonation/deprotonation events, H-bonding, and geometrical constraints imparted by the rigidity of the foldamer backbone. Compared to tartaric acid, binding of 2,2-difluorosuccinic acid or 2,2,3,3-tetrafluorosuccinic acid resulted in symmetry breaking due to deprotonation of only one of the two carboxylic acid groups of the encapsulated species as shown by NMR studies in solution and by single-crystal X-ray diffraction in the solid state. An analogous 14-mer foldamer capsule terminated with a thiol anchoring group was used to probe the complexation event in self-assembled monolayers on Au substrates. Ellipsometry and polarization-modulation infrared absorption-reflection spectroscopy studies were consistent with the formation of a single molecule layer of the foldamer capsule oriented vertically with respect to the surface. The latter underwent smooth complexation of 2,2-difluorosuccinic acid with deprotonation of one of the two carboxylic acid groups. A significant (80-fold) difference in the charge transport properties of the monolayer upon encapsulation of the dicarboxylic acid was evidenced from conducting-AFM measurements (S = 1.1 × 10-9 vs. 1.4 × 10-11 ohm-1 for the empty and complexed capsule, respectively). The modulation in conductivity was assigned to protonation of the aromatic foldamer backbone.
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Affiliation(s)
- Pedro Mateus
- Univ. Bordeaux, CNRS, Bordeaux INP, UMR 5248 CBMN, IECB 2 rue Escarpit 33600 Pessac France
| | - Antoine Jacquet
- Univ. Bordeaux, CNRS, Bordeaux INP, UMR 5248 CBMN, IECB 2 rue Escarpit 33600 Pessac France
| | | | - Alice Boulloy
- Univ. Bordeaux, CNRS, Bordeaux INP, UMR 5248 CBMN, IECB 2 rue Escarpit 33600 Pessac France
| | - Brice Kauffmann
- Univ. Bordeaux, CNRS UMS 3033/US001 IECB 2 rue Escarpit 33600 Pessac France
| | - Gilles Pecastaings
- Inst. Polytechnique de Bordeaux, CNRS UMR 5629 LCPO 16, Av. Pey-Berland 33600 Pessac France
| | - Thierry Buffeteau
- Univ. Bordeaux, CNRS UMR 5255 ISM 351, Cours de la Libération 33405 Talence France
| | - Yann Ferrand
- Univ. Bordeaux, CNRS, Bordeaux INP, UMR 5248 CBMN, IECB 2 rue Escarpit 33600 Pessac France
| | - Dario M Bassani
- Univ. Bordeaux, CNRS UMR 5255 ISM 351, Cours de la Libération 33405 Talence France
| | - Ivan Huc
- Univ. Bordeaux, CNRS, Bordeaux INP, UMR 5248 CBMN, IECB 2 rue Escarpit 33600 Pessac France
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandstraße 5-13 81377 Munich Germany
- Cluster of Excellence e-Conversion 85748 Garching Germany
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19
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Maciá E. Base-Pairs' Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E5119. [PMID: 33202814 PMCID: PMC7697525 DOI: 10.3390/ma13225119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 05/12/2023]
Abstract
By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson-Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons' dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.
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Affiliation(s)
- Enrique Maciá
- Departamento de Física de Materiales, Facultad CC. Físicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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20
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Dwyer DS. Genomic Chaos Begets Psychiatric Disorder. Complex Psychiatry 2020; 6:20-29. [PMID: 34883501 PMCID: PMC7673594 DOI: 10.1159/000507988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/06/2020] [Indexed: 12/21/2022] Open
Abstract
The processes that created the primordial genome are inextricably linked to current day vulnerability to developing a psychiatric disorder as summarized in this review article. Chaos and dynamic forces including duplication, transposition, and recombination generated the protogenome. To survive early stages of genome evolution, self-organization emerged to curb chaos. Eventually, the human genome evolved through a delicate balance of chaos/instability and organization/stability. However, recombination coldspots, silencing of transposable elements, and other measures to limit chaos also led to retention of variants that increase risk for disease. Moreover, ongoing dynamics in the genome creates various new mutations that determine liability for psychiatric disorders. Homologous recombination, long-range gene regulation, and gene interactions were all guided by spooky action-at-a-distance, which increased variability in the system. A probabilistic system of life was required to deal with a changing environment. This ensured the generation of outliers in the population, which enhanced the probability that some members would survive unfavorable environmental impacts. Some of the outliers produced through this process in man are ill suited to cope with the complex demands of modern life. Genomic chaos and mental distress from the psychological challenges of modern living will inevitably converge to produce psychiatric disorders in man.
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Affiliation(s)
- Donard S. Dwyer
- Departments of Psychiatry and Behavioral Medicine and Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, Louisiana, USA
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21
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Huang Q, Li J, Shi T, Liang J, Wang Z, Bai L, Deng Z, Zhao YL. Defense Mechanism of Phosphorothioated DNA under Peroxynitrite-Mediated Oxidative Stress. ACS Chem Biol 2020; 15:2558-2567. [PMID: 32816442 DOI: 10.1021/acschembio.0c00591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA phosphorothioation (PT) exists in many pathogenic bacteria; however, the mechanism of PT-DNA resistance to the immune response is unclear. In this work, we meticulously investigated the peroxynitrite (PN) tolerance using PT-bioengineered E. coli strains. The in vivo experiment confirms that the S+ strain survives better than the S- strain under moderately oxidative stress. The LCMS, IC, and GCMS experiments demonstrated that phosphorothioate partially converted to phosphate, and the byproduct included sulfate and elemental sulfur. When O,O-diethyl thiophosphate ester (DETP) was used, the reaction rate k1 was determined to be 4.3 ± 0.5 M-1 s-1 in the first-order for both phosphorothioate and peroxynitrite at 35 °C and pH of 8.0. The IC50 values of phosphorothioate dinucleotides are dramatically increased by 400-700-fold compared to DETP. The SH/OH Yin-Yang mechanism rationalizes the in situ DNA self-defense against PN-mediated oxidative stress at the extra bioenergetic cost of DNA modification.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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22
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23
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Goodchild SA, Gao R, Shenton DP, McIntosh AJS, Brown T, Bartlett PN. Direct Detection and Discrimination of Nucleotide Polymorphisms Using Anthraquinone Labeled DNA Probes. Front Chem 2020; 8:381. [PMID: 32478035 PMCID: PMC7235368 DOI: 10.3389/fchem.2020.00381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/14/2020] [Indexed: 02/04/2023] Open
Abstract
A novel electrochemical detection approach using DNA probes labeled with Anthraquinone (AQ) as a reporter moiety has been successfully exploited as a method for the direct detection of DNA targets. This assay uses simple voltammetry techniques (Differential Pulse Voltammetry) to exploit the unique responsiveness of AQ to its chemical environments within oxygenated aqueous buffers, providing a specific detection mechanism as a result of DNA hybridization. This measurement is based on a cathodic shift of the reduction potential of the AQ tag and the concurrent reduction in peak current upon DNA binding. The further utility of this approach for discrimination of closely related DNA targets is demonstrated using DNA strands specific to B. anthracis and closely related bacillus species. DNA targets were designed to the rpoB gene incorporating nucleotide polymorphisms associated with different bacillus species. This assay was used to demonstrate that the shift in reduction potential is directly related to the homology of the target DNA. The discriminatory mechanism is dependent on the presence of oxygen in the measurement buffer and is strongly linked to the position of the nucleotide polymorphisms; with homology at the terminus carrying the AQ functionalised nucleotide critical to achieving accurate discrimination. This understanding of assay design was used to demonstrate an optimized assay capable of discriminating between Yersinia pestis (the causative agent of plague) and closely related species based on the groEL gene. This method is attractive as it can not only detect DNA binding, but can also discriminate between multiple Single Nucleotide Polymorphisms (SNPs) within that DNA without the need for any additional reagents, reporters, or processes such as melting of DNA strands. This indicates that this approach may have great potential to be exploited within novel biosensors for detection and diagnosis of infectious disease in future Point of Care (PoC) devices.
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Affiliation(s)
- Sarah A Goodchild
- Defence Science and Technology Laboratory, Salisbury, United Kingdom.,University of Southampton, Southampton, United Kingdom
| | - Rachel Gao
- University of Southampton, Southampton, United Kingdom
| | - Daniel P Shenton
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | | | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Philip N Bartlett
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
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24
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Xu W, Jin T, Dai Y, Liu CC. Surpassing the detection limit and accuracy of the electrochemical DNA sensor through the application of CRISPR Cas systems. Biosens Bioelectron 2020; 155:112100. [PMID: 32090878 DOI: 10.1016/j.bios.2020.112100] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/26/2022]
Abstract
Robust developments of personalized medicine for next-generation healthcare highlight the need for sensitive and accurate point-of-care platforms for quantification of disease biomarkers. Broad presentations of clustered regularly interspaced short palindromic repeats (CRISPR) as an accurate gene editing tool also indicate that the high-specificity and programmability of CRISPR system can be utilized for the development of biosensing systems. Herein, we present a CRISPR Cas system enhanced electrochemical DNA (E-DNA) sensor with unprecedented sensitivity and accuracy. The principle of the E-DNA sensor is the target induced conformational change of the surface signaling probe (containing an electrochemical tag), leading to the variation of the electron transfer rate of the electrochemical tag. With the introduction of CRISPR cleavage activity into the E-DNA sensor, a more apparent signal change between with and without the presence of the target can be achieved. We compared the performance of Cas9 and Cas12a enhanced E-DNA sensor and optimized the chemical environment of CRISPR, achieving a femto-molar detection limit without enzymatic amplification. Moreover, we correlated the CRISPR cleavage signal with the original E-DNA signal as a strategy to indicate potential mismatches in the target sequence. Comparing with classic DNA electrochemistry based mutation detection strategy, CRISPR enhanced E-DNA sensor can determine the presence of a single mutation at an unknown concentration condition. Overall, we believe that the CRISPR enhanced E-DNA sensing strategy will be of especially high utility for point-of-care systems owing to the programmability, modularity, high-sensitivity and high-accuracy.
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Affiliation(s)
- Wei Xu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Tian Jin
- College of Biological Sciences, University of California, Davis, CA, 95616, USA
| | - Yifan Dai
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA; Electronics Design Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Chung Chiun Liu
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA; Electronics Design Center, Case Western Reserve University, Cleveland, OH, 44106, USA
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25
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Fukuhara G. Analytical supramolecular chemistry: Colorimetric and fluorimetric chemosensors. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2020.100340] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Miyagawa A, Eng J, Okada T, Inoue Y, Penfold TJ, Fukuhara G. Hydrostatic Pressure-Induced Spectral Variation of Reichardt's Dye: A Polarity/Pressure Dual Indicator. ACS OMEGA 2020; 5:897-903. [PMID: 31956843 PMCID: PMC6964516 DOI: 10.1021/acsomega.9b03880] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
The famous solvatochromic Reichardt's dye was applied to quantify hydrostatic pressure in media. The UV/vis spectra of the dye in various organic solvents are shifted bathochromically or hypsochromically at the shorter- or longer-wavelength band, respectively, upon hydrostatic pressurization. The E T value, determined by an absorption maximum, in ethyl acetate increases from 38.5 kcal mol-1 at 0.1 MPa to 39.2 kcal mol-1 at 300 MPa, which is mostly equal to the one in chloroform at 0.1 MPa. These spectroscopic origins were supported by the time-dependent density functional theory (TD-DFT) calculations. The concept and approach proposed in this paper, i.e., a dual indicator, should attract the attention of a broad spectrum in multidisciplinary science.
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Affiliation(s)
- Akihisa Miyagawa
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Julien Eng
- Chemistry-
School of Natural and Environmental Sciences, Newcastle University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Tetsuo Okada
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yoshihisa Inoue
- Department
of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Thomas James Penfold
- Chemistry-
School of Natural and Environmental Sciences, Newcastle University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Gaku Fukuhara
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- JST,
PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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27
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28
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The influence of monovalent and divalent metal cations on the stability of the DNA-protein interaction in the nucleosome core particle. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Dai Y, Somoza RA, Wang L, Welter JF, Li Y, Caplan AI, Liu CC. Exploring the Trans-Cleavage Activity of CRISPR-Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor. Angew Chem Int Ed Engl 2019; 58:17399-17405. [PMID: 31568601 PMCID: PMC6938695 DOI: 10.1002/anie.201910772] [Citation(s) in RCA: 323] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/23/2019] [Indexed: 12/18/2022]
Abstract
An accurate, rapid, and cost-effective biosensor for the quantification of disease biomarkers is vital for the development of early-diagnostic point-of-care systems. The recent discovery of the trans-cleavage property of CRISPR type V effectors makes CRISPR a potential high-accuracy bio-recognition tool. Herein, a CRISPR-Cas12a (cpf1) based electrochemical biosensor (E-CRISPR) is reported, which is more cost-effective and portable than optical-transduction-based biosensors. Through optimizing the in vitro trans-cleavage activity of Cas12a, E-CRIPSR was used to detect viral nucleic acids, including human papillomavirus 16 (HPV-16) and parvovirus B19 (PB-19), with a picomolar sensitivity. An aptamer-based E-CRISPR cascade was further designed for the detection of transforming growth factor β1 (TGF-β1) protein in clinical samples. As demonstrated, E-CRISPR could enable the development of portable, accurate, and cost-effective point-of-care diagnostic systems.
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Affiliation(s)
- Yifan Dai
- Department of Chemical and Biomolecular Engineering, Electronics Design Center, Case Western Reserve University; Cleveland, Ohio, 44106 (USA)
| | - Rodrigo A Somoza
- Department of Biology, Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Liu Wang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Jean F Welter
- Department of Biology, Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Arnold I Caplan
- Department of Biology, Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Chung Chiun Liu
- Department of Chemical and Biomolecular Engineering, Electronics Design Center, Case Western Reserve University; Cleveland, Ohio, 44106 (USA)
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30
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Dai Y, Somoza RA, Wang L, Welter JF, Li Y, Caplan AI, Liu CC. Exploring the Trans‐Cleavage Activity of CRISPR‐Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910772] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yifan Dai
- Department of Chemical and Biomolecular Engineering, Electronics Design CenterCase Western Reserve University Cleveland OH 44106 USA
| | - Rodrigo A Somoza
- Department of Biology, Skeletal Research Center &, Center for Multimodal Evaluation of Engineered CartilageCase Western Reserve University Cleveland OH 44106 USA
| | - Liu Wang
- Department of Genetics and Genome SciencesSchool of MedicineCase Western Reserve University Cleveland OH 44106 USA
| | - Jean F. Welter
- Department of Biology, Skeletal Research Center &, Center for Multimodal Evaluation of Engineered CartilageCase Western Reserve University Cleveland OH 44106 USA
| | - Yan Li
- Department of Genetics and Genome SciencesSchool of MedicineCase Western Reserve University Cleveland OH 44106 USA
| | - Arnold I Caplan
- Department of Biology, Skeletal Research Center &, Center for Multimodal Evaluation of Engineered CartilageCase Western Reserve University Cleveland OH 44106 USA
| | - Chung Chiun Liu
- Department of Chemical and Biomolecular Engineering, Electronics Design CenterCase Western Reserve University Cleveland OH 44106 USA
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31
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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32
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Kogikoski S, Paschoalino WJ, Cantelli L, Silva W, Kubota LT. Electrochemical sensing based on DNA nanotechnology. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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33
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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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34
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Wu G, Liu Y, Yang Z, Katakam N, Rouh H, Ahmed S, Unruh D, Surowiec K, Li G. Multilayer 3D Chirality and Its Synthetic Assembly. RESEARCH 2019; 2019:6717104. [PMID: 31549078 PMCID: PMC6750085 DOI: 10.34133/2019/6717104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/23/2019] [Indexed: 12/31/2022]
Abstract
3D chirality of sandwich type of organic molecules has been discovered. The key element of this chirality is characterized by three layers of structures that are arranged nearly in parallel fashion with one on top and one down from the center plane. Individual enantiomers of these molecules have been fully characterized by spectroscopies with their enantiomeric purity measured by chiral HPLC. The absolute configuration was unambiguously assigned by X-ray diffraction analysis. This is the first multilayer 3D chirality reported and is anticipated to lead to a new research area of asymmetric synthesis and catalysis and to have a broad impact on chemical, medicinal, and material sciences in future.
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Affiliation(s)
- Guanzhao Wu
- Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Yangxue Liu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Zhen Yang
- Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Nandakumar Katakam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Hossein Rouh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Sultan Ahmed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Daniel Unruh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Kazimierz Surowiec
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Guigen Li
- Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
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35
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Sun H, Zheng L, Yang K, Greenberg MM. Positional Dependence of DNA Hole Transfer Efficiency in Nucleosome Core Particles. J Am Chem Soc 2019; 141:10154-10158. [PMID: 31244168 DOI: 10.1021/jacs.9b03686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Electron deficient "holes" migrate over long distances through the π-system in free DNA. Hole transfer efficiency (HTE) is strongly dependent on sequence and π-stacking. However, there is no consensus regarding the effects of nucleosome core particle (NCP) environment on hole migration. We quantitatively determined HTE in free DNA and NCPs by independently generating holes at specific positions in DNA. The relative HTE varied widely with respect to position within the NCP and proximity to tyrosine, which suppresses hole transfer. These data indicate that hole transfer in chromatin will be affected by the DNA sequence and its position with respect to histone proteins within NCPs.
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Affiliation(s)
- Huabing Sun
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
| | - Liwei Zheng
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
| | - Kun Yang
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
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36
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Raetz AG, David SS. When you're strange: Unusual features of the MUTYH glycosylase and implications in cancer. DNA Repair (Amst) 2019; 80:16-25. [PMID: 31203172 DOI: 10.1016/j.dnarep.2019.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023]
Abstract
MUTYH is a base-excision repair glycosylase that removes adenine opposite 8-oxoguanine (OG). Variants of MUTYH defective in functional activity lead to MUTYH-associated polyposis (MAP), which progresses to cancer with very high penetrance. Whole genome and whole exome sequencing studies have found MUTYH deficiencies in an increasing number of cancer types. While the canonical OG:A repair activity of MUTYH is well characterized and similar to bacterial MutY, here we review more recent evidence that MUTYH has activities independent of OG:A repair and appear centered on the interdomain connector (IDC) region of MUTYH. We summarize evidence that MUTYH is involved in rapid DNA damage response (DDR) signaling, including PARP activation, 9-1-1 and ATR signaling, and SIRT6 activity. MUTYH alters survival and DDR to a wide variety of DNA damaging agents in a time course that is not consistent with the formation of OG:A mispairs. Studies that suggest MUTYH inhibits the repair of alkyl-DNA damage and cyclopyrimidine dimers (CPDs) is reviewed, and evidence of a synthetic lethal interaction with mismatch repair (MMR) is summarized. Based on these studies we suggest that MUTYH has evolved from an OG:A mispair glycosylase to a multifunctional scaffold for DNA damage response signaling.
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Affiliation(s)
- Alan G Raetz
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Sheila S David
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
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37
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Song J, Ni J, Wang Q, Chen H, Gao F, Lin Z, Wang Q. A planar and uncharged copper(II)-picolinic acid chelate: Its intercalation to duplex DNA by experimental and theoretical studies and electrochemical sensing application. Biosens Bioelectron 2019; 141:111405. [PMID: 31195198 DOI: 10.1016/j.bios.2019.111405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 11/28/2022]
Abstract
Using an external redox-active molecule as a DNA hybridization indicator is still a popular strategy in electrochemical DNA biosensors because it is label-free and the multi-site binding can enhance the response signal. A planar and uncharged transition metal complex, Cu(PA)2 (PA = picolinic acid) with excellent electrochemical activity has been synthesized and its interaction with double-stranded DNA (dsDNA) is studied by experimental electrochemical methods and theoretical molecular docking technology. The experimental results reveal that the copper complex interacts with dsDNA via specific intercalation, which is verified by the molecular docking result. The surface-based voltammetric analysis demonstrates that the planar Cu(PA)2 can effectively accumulate within the electrode-confined hybridized duplex DNA rather than the single-stranded probe DNA. Based on this phenomenon, the Cu(PA)2 is utilized as an electrochemical hybridization indicator for the detection of oligonucleotides. The sensing assays show that upon incubation in Cu(PA)2 solution, the probe electrode does not display any Faraday signal, but the hybridized one has a pair of strong redox peaks corresponding to the electrochemistry of Cu(PA)2, showing excellent hybridization indicating function of Cu(PA)2 without background interference. The signal intensity of Cu(PA)2 is dependent on the concentrations of the target oligonucleotide ranging from 1 fM to 100 nM with an experimental detection limit of 1.0 fM. Due to the specific intercalation of Cu(PA)2 with dsDNA, the biosensor also exhibits good ability to recognize oligonucleotide with different base mismatching degree.
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Affiliation(s)
- Juan Song
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China
| | - Jiancong Ni
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China; Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, 350116, China
| | - Qinghua Wang
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China
| | - Huangcan Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Feng Gao
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China
| | - Zhenyu Lin
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China; Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, 350116, China
| | - Qingxiang Wang
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China.
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38
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Abendroth JM, Stemer DM, Bloom BP, Roy P, Naaman R, Waldeck DH, Weiss PS, Mondal PC. Spin Selectivity in Photoinduced Charge-Transfer Mediated by Chiral Molecules. ACS NANO 2019; 13:4928-4946. [PMID: 31016968 DOI: 10.1021/acsnano.9b01876] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Optical control and readout of electron spin and spin currents in thin films and nanostructures have remained attractive yet challenging goals for emerging technologies designed for applications in information processing and storage. Recent advances in room-temperature spin polarization using nanometric chiral molecular assemblies suggest that chemically modified surfaces or interfaces can be used for optical spin conversion by exploiting photoinduced charge separation and injection from well-coupled organic chromophores or quantum dots. Using light to drive photoexcited charge-transfer processes mediated by molecules with central or helical chirality enables indirect measurements of spin polarization attributed to the chiral-induced spin selectivity effect and of the efficiency of spin-dependent electron transfer relative to competitive relaxation pathways. Herein, we highlight recent approaches used to detect and to analyze spin selectivity in photoinduced charge transfer including spin-transfer torque for local magnetization, nanoscale charge separation and polarization, and soft ferromagnetic substrate magnetization- and chirality-dependent photoluminescence. Building on these methods through systematic investigation of molecular and environmental parameters that influence spin filtering should elucidate means to manipulate electron spins and photoexcited states for room-temperature optoelectronic and photospintronic applications.
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Affiliation(s)
- John M Abendroth
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Dominik M Stemer
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Materials Science and Engineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Brian P Bloom
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Partha Roy
- Department of Chemistry , Central University of Rajasthan , Kishangarh 305817 Ajmer , India
| | - Ron Naaman
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - David H Waldeck
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Paul S Weiss
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Materials Science and Engineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
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Lin K, Burke A, King NB, Kahanda D, Mazaheripour A, Bartlett A, Dibble DJ, McWilliams MA, Taylor DW, Jocson J, Minary‐Jolandan M, Gorodetsky AA, Slinker JD. Enhancement of the Electrical Properties of DNA Molecular Wires through Incorporation of Perylenediimide DNA Base Surrogates. Chempluschem 2019; 84:416-419. [DOI: 10.1002/cplu.201800661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/27/2019] [Indexed: 01/30/2023]
Affiliation(s)
- Kuo‐Yao Lin
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Anthony Burke
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Nolan B. King
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Dimithree Kahanda
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - David J. Dibble
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Marc A. McWilliams
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - David W. Taylor
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Majid Minary‐Jolandan
- Department of Mechanical Engineering The University of Texas at Dallas 800 W. Campbell Road, EC 38 Richardson TX 75080-3020 USA
| | - Alon A. Gorodetsky
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Jason D. Slinker
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
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40
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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41
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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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43
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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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