1
|
Deng L, Bhat IH, Guo AM. Spin-selectivity effect of G-quadruplex DNA molecules. J Chem Phys 2023; 158:244116. [PMID: 37377158 DOI: 10.1063/5.0156389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Chirality-induced spin selectivity has been attracting extensive interest in recent years and is demonstrated in a variety of chiral molecules, all of which arise from inherent molecular chirality. Here, we first propose a theoretical model to study the spin-dependent electron transport along guanine-quadruplex (G4) DNA molecules, connected to two nonmagnetic electrodes, by considering the molecule-electrode contact and weak spin-orbit coupling. Our results indicate that the G4-DNA molecular junctions exhibit pronounced spin-selectivity effect, and the asymmetric contact-induced external chirality, instead of the inherent molecular chirality, dominates their spin filtration efficiency. Furthermore, the spin-selectivity effect is robust against the disorder and hold in a wide range of model parameters. These results could be checked by charge transport measurements and provide an alternative way to improve the spin-selectivity effect of chiral nanodevices.
Collapse
Affiliation(s)
- Lei Deng
- Hunan Key Laboratory for Super-microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China
| | - Irfan Hussain Bhat
- Hunan Key Laboratory for Super-microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China
| | - Ai-Min Guo
- Hunan Key Laboratory for Super-microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China
| |
Collapse
|
2
|
Deiana M, Chand K, Chorell E, Sabouri N. Parallel G-Quadruplex DNA Structures from Nuclear and Mitochondrial Genomes Trigger Emission Enhancement in a Nonfluorescent Nano-aggregated Fluorine-Boron-Based Dye. J Phys Chem Lett 2023; 14:1862-1869. [PMID: 36779779 PMCID: PMC9940295 DOI: 10.1021/acs.jpclett.2c03301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/02/2023] [Indexed: 05/28/2023]
Abstract
Molecular self-assembly is a powerful tool for the development of functional nanostructures with adaptive optical properties. However, in aqueous solution, the hydrophobic effects in the monomeric units often afford supramolecular architectures with typical side-by-side π-stacking arrangement with compromised emissive properties. Here, we report on the role of parallel DNA guanine quadruplexes (G4s) as supramolecular disaggregating-capture systems capable of coordinating a zwitterionic fluorine-boron-based dye and promoting activation of its fluorescence signal. The dye's high binding affinity for parallel G4s compared to nonparallel topologies leads to a selective disassembly of the dye's supramolecular state upon contact with parallel G4s. This results in a strong and selective disaggregation-induced emission that signals the presence of parallel G4s observable by the naked eye and inside cells. The molecular recognition strategy reported here will be useful for a multitude of affinity-based applications with potential in sensing and imaging systems.
Collapse
Affiliation(s)
- Marco Deiana
- Department
of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Karam Chand
- Department
of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Erik Chorell
- Department
of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Nasim Sabouri
- Department
of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| |
Collapse
|
3
|
Hart SM, Banal JL, Castellanos MA, Markova L, Vyborna Y, Gorman J, Häner R, Willard AP, Bathe M, Schlau-Cohen GS. Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds. Chem Sci 2022; 13:13020-13031. [PMID: 36425503 PMCID: PMC9667922 DOI: 10.1039/d2sc02759c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/04/2022] [Indexed: 09/16/2023] Open
Abstract
Strongly-coupled multichromophoric assemblies orchestrate the absorption, transport, and conversion of photonic energy in natural and synthetic systems. Programming these functionalities involves the production of materials in which chromophore placement is precisely controlled. DNA nanomaterials have emerged as a programmable scaffold that introduces the control necessary to select desired excitonic properties. While the ability to control photophysical processes, such as energy transport, has been established, similar control over photochemical processes, such as interchromophore charge transfer, has not been demonstrated in DNA. In particular, charge transfer requires the presence of close-range interchromophoric interactions, which have a particularly steep distance dependence, but are required for eventual energy conversion. Here, we report a DNA-chromophore platform in which long-range excitonic couplings and short-range charge-transfer couplings can be tailored. Using combinatorial screening, we discovered chromophore geometries that enhance or suppress photochemistry. We combined spectroscopic and computational results to establish the presence of symmetry-breaking charge transfer in DNA-scaffolded squaraines, which had not been previously achieved in these chromophores. Our results demonstrate that the geometric control introduced through the DNA can access otherwise inaccessible processes and program the evolution of excitonic states of molecular chromophores, opening up opportunities for designer photoactive materials for light harvesting and computation.
Collapse
Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Maria A Castellanos
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Larysa Markova
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Yuliia Vyborna
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | | |
Collapse
|
4
|
Barclay MS, Wilson CK, Roy SK, Mass OA, Obukhova OM, Svoiakov RP, Tatarets AL, Chowdhury AU, Huff JS, Turner DB, Davis PH, Terpetschnig EA, Yurke B, Knowlton WB, Lee J, Pensack RD. Oblique Packing and Tunable Excitonic Coupling in DNA‐Templated Squaraine Rotaxane Dimer Aggregates. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Matthew S. Barclay
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Christopher K. Wilson
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Simon K. Roy
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Olga A. Mass
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Olena M. Obukhova
- SSI Institute for Single Crystals NAS of Ukraine: Naukovo-tehnologicnij kompleks Institut monokristaliv Nacional'na akademia nauk Ukraini Department of Luminescent Materials and Dyes UKRAINE
| | - Rostyslav P. Svoiakov
- SSI Institute for Single Crystals NAS of Ukraine: Naukovo-tehnologicnij kompleks Institut monokristaliv Nacional'na akademia nauk Ukraini Department of Luminescent Materials and Dyes UKRAINE
| | - Anatoliy L. Tatarets
- SSI Institute for Single Crystals NAS of Ukraine: Naukovo-tehnologicnij kompleks Institut monokristaliv Nacional'na akademia nauk Ukraini Department of Luminescent Materials and Dyes UKRAINE
| | - Azhad U. Chowdhury
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Jonathan S. Huff
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Daniel B. Turner
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Paul H. Davis
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | | | - Bernard Yurke
- Boise State University Micron School of Materials Science & Engineering; Department of Electrical & Computer Engineering UNITED STATES
| | - William B. Knowlton
- Boise State University Micron School of Materials Science & Engineering; Department of Electrical & Computer Engineering UNITED STATES
| | - Jeunghoon Lee
- Boise State University Micron School of Materials Science & Engineering; Department of Chemistry & Biochemistry UNITED STATES
| | - Ryan D. Pensack
- Boise State University Micron School of Materials Science & Engineering 1435 W University Dr 83706 Boise UNITED STATES
| |
Collapse
|
5
|
Pavc D, Sebastian N, Spindler L, Drevenšek-Olenik I, Podboršek GK, Plavec J, Šket P. Understanding self-assembly at molecular level enables controlled design of DNA G-wires of different properties. Nat Commun 2022; 13:1062. [PMID: 35217667 PMCID: PMC8881451 DOI: 10.1038/s41467-022-28726-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
A possible engineering of materials with diverse bio- and nano-applications relies on robust self-assembly of oligonucleotides. Bottom-up approach utilizing guanine-rich DNA oligonucleotides can lead to formation of G-wires, nanostructures consisting of continuous stacks of G-quartets. However, G-wire structure and self-assembly process remain poorly understood, although they are crucial for optimizing properties needed for specific applications. Herein, we use nuclear magnetic resonance to get insights at molecular level on how chosen short, guanine-rich oligonucleotides self-assemble into G-wires, whereas complementary methods are used for their characterization. Additionally, unravelling mechanistic details enable us to guide G-wire self-assembly in a controlled manner. MD simulations provide insight why loop residues with considerably different properties, i.e., hydrogen-bond affinity, stacking interactions, electronic effects and hydrophobicity extensively increase or decrease G-wire length. Our results provide fundamental understanding of G-wire self-assembly process useful for future design of nanomaterials with specific properties. G-wire structures have potential applications in bio-nanotechnology, however, this is limited by a lack of understanding about the assembly process and structures formed. Here, the authors use nuclear magnetic resonance and molecular dynamic simulations to understand the guiding principles of G-wire assembly.
Collapse
Affiliation(s)
- Daša Pavc
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Nerea Sebastian
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia
| | - Lea Spindler
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia.,Faculty of Mechanical Engineering, University of Maribor, 2000, Maribor, Slovenia
| | - Irena Drevenšek-Olenik
- Department of Complex Matter, Jožef Stefan Institute, 1000, Ljubljana, Slovenia.,Faculty of Mathematics and Physics, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Gorazd Koderman Podboršek
- Department of Materials Chemistry, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.,EN-FIST, Center of Excellence, 1000, Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia.
| |
Collapse
|
6
|
Balanikas E, Martinez-Fernandez L, Baldacchino G, Markovitsi D. Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups. Int J Mol Sci 2021; 22:ijms222413436. [PMID: 34948235 PMCID: PMC8704496 DOI: 10.3390/ijms222413436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3' or 5' ends. This position also affects significantly the electronic absorption spectrum of (G+)● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)● radicals and, on the other, they give rise to a reaction product absorbing in the 300-500 nm spectral domain.
Collapse
Affiliation(s)
- Evangelos Balanikas
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Lara Martinez-Fernandez
- Departamento de Química, Modúlo 13, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Correspondence: (L.M.-F.); or (D.M.)
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
- Correspondence: (L.M.-F.); or (D.M.)
| |
Collapse
|
7
|
Manoli F, Doria F, Colombo G, Zambelli B, Freccero M, Manet I. The Binding Pocket at the Interface of Multimeric Telomere G-quadruplexes: Myth or Reality? Chemistry 2021; 27:11707-11720. [PMID: 34152657 PMCID: PMC8456957 DOI: 10.1002/chem.202101486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 01/23/2023]
Abstract
Human telomeric DNA with hundreds of repeats of the 5'-TTAGGG-3' motif plays a crucial role in several biological processes. It folds into G-quadruplex (G4) structures and features a pocket at the interface of two contiguous G4 blocks. Up to now no structural NMR and crystallographic data are available for ligands interacting with contiguous G4s. Naphthalene diimide monomers and dyads were investigated as ligands of a dimeric G4 of human telomeric DNA comparing the results with those of the model monomeric G4. Time-resolved fluorescence, circular dichroism, isothermal titration calorimetry and molecular modeling were used to elucidate binding features. Ligand fluorescence lifetime and induced circular dichroism unveiled occupancy of the binding site at the interface. Thermodynamic parameters confirmed the hypothesis as they remarkably change for the dyad complexes of the monomeric and dimeric telomeric G4. The bi-functional ligand structure of the dyads is a fundamental requisite for binding at the G4 interface as only the dyads engage in complexes with 1 : 1 stoichiometry, lodging in the pocket at the interface and establishing multiple interactions with the DNA skeleton. In the absence of NMR and crystallographic data, our study affords important proofs of binding at the interface pocket and clues on the role played by the ligand structure.
Collapse
Affiliation(s)
- Francesco Manoli
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR)Via P. Gobetti 10140129BolognaItaly
| | - Filippo Doria
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Giorgio Colombo
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Barbara Zambelli
- Department of Pharmacy and BiotechnologyUniversity of BolognaV. le Fanin 4040127BolognaItaly
| | - Mauro Freccero
- Department of ChemistryUniversity of PaviaV. le Taramelli 1027100PaviaItaly
| | - Ilse Manet
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR)Via P. Gobetti 10140129BolognaItaly
| |
Collapse
|
8
|
Milovanović B, Etinski M, Popov I. Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study. NANOTECHNOLOGY 2021; 32:435405. [PMID: 34284367 DOI: 10.1088/1361-6528/ac162c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.
Collapse
Affiliation(s)
- Branislav Milovanović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Igor Popov
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, Belgrade, Serbia
- Institut of Physics, University of Belgrade, Pregrevica 118, Belgrade, Serbia
| |
Collapse
|
9
|
Krul SE, Hoehn SJ, Feierabend KJ, Crespo-Hernández CE. Excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate. J Chem Phys 2021; 154:075103. [PMID: 33607894 DOI: 10.1063/5.0038123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Minor structural modifications to the DNA and RNA nucleobases have a significant effect on their excited state dynamics and electronic relaxation pathways. In this study, the excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate are investigated in aqueous solution and in a mixture of methanol and water using femtosecond broadband transient absorption spectroscopy following excitation at 267 nm. The transient spectra are collected using photon densities that ensure no parasitic multiphoton-induced signal from solvated electrons. The data can be fit satisfactorily using a two- or three-component kinetic model. By analyzing the results from steady-state, time-resolved, computational calculations, and the methanol-water mixture, the following general relaxation mechanism is proposed for both molecules, Lb → La → 1πσ*(ICT) → S0, where the 1πσ*(ICT) stands for an intramolecular charge transfer excited singlet state with significant πσ* character. In general, longer lifetimes for internal conversion are obtained for 7-deazaguanosine compared to guanosine 5'-monophosphate. Internal conversion of the 1πσ*(ICT) state to the ground state occurs on a similar time scale of a few picoseconds in both molecules. Collectively, the results demonstrate that substitution of a single nitrogen atom for a methine (C-H) group at position seven of the guanine moiety stabilizes the 1ππ* Lb and La states and alters the topology of their potential energy surfaces in such a way that the relaxation dynamics in 7-deazaguanosine are slowed down compared to those in guanosine 5'-monophosphate but not for the internal conversion of 1πσ*(ICT) state to the ground state.
Collapse
Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Karl J Feierabend
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | | |
Collapse
|
10
|
Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions. Molecules 2020; 25:molecules25092094. [PMID: 32365780 PMCID: PMC7248781 DOI: 10.3390/molecules25092094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
The study deals with the primary species, ejected electrons, and guanine radicals, leading to oxidative damage, that is generated in four-stranded DNA structures (guanine quadruplexes) following photo-ionization by low-energy UV radiation. Performed by nanosecond transient absorption spectroscopy with 266 nm excitation, it focusses on quadruplexes formed by folding of GGG(TTAGGG)3 single strands in the presence of K+ ions, TEL21/K+. The quantum yield for one-photon ionization (9.4 × 10-3) was found to be twice as high as that reported previously for TEL21/Na+. The overall population of guanine radicals decayed faster, their half times being, respectively, 1.4 and 6.7 ms. Deprotonation of radical cations extended over four orders of magnitude of time; the faster step, concerning 40% of their population, was completed within 500 ns. A reaction intermediate, issued from radicals, whose absorption spectrum peaked around 390 nm, was detected.
Collapse
Affiliation(s)
- Evangelos Balanikas
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
| | - Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France; (E.B.); (A.B.); (G.B.)
- Correspondence: ; Tel.: +33-169084644
| |
Collapse
|
11
|
Martínez-Fernández L, Esposito L, Improta R. Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives. Photochem Photobiol Sci 2020; 19:436-444. [DOI: 10.1039/d0pp00065e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.
Collapse
Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química
- Facultad de Ciencias
- Modulo 13 Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC Cantoblanco
- 28049 Madrid
| | | | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini
- CNR
- I-80134 Napoli
- Italy
| |
Collapse
|
12
|
Reveguk ZV, Khoroshilov EV, Sharkov AV, Pomogaev VA, Buglak AA, Tarnovsky AN, Kononov AI. Exciton Absorption and Luminescence in i-Motif DNA. Sci Rep 2019; 9:15988. [PMID: 31690734 PMCID: PMC6831829 DOI: 10.1038/s41598-019-52242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/17/2019] [Indexed: 11/08/2022] Open
Abstract
We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC)10, using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.3 eV) red shift of the lowest-energy transition in the i-motif form relative to its absorption maximum, which agrees with the experimental absorption spectrum. The lowest excitonic state in i-(dC)10 is responsible for a 2 ps red-shifted emission at 370 nm observed in the decay-associated spectra obtained on the femtosecond time-scale. This delocalized (excitonic) excited state is likely a precursor to a long-lived excimer state observed in previous studies. Another fast 310 fs component at 330 nm is assigned to a monomer-like locally excited state. Both emissive states form within less than the available time resolution of the instrument (100 fs). This work contributes to the understanding of excited-state dynamics of DNA within the first few picoseconds, which is the most interesting time range with respect to unraveling the photodamage mechanism, including the formation of the most dangerous DNA lesions such as cyclobutane pyrimidine dimers.
Collapse
Affiliation(s)
- Zakhar V Reveguk
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia
| | - Evgeny V Khoroshilov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991, Moscow, Russia
| | - Andrey V Sharkov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991, Moscow, Russia
| | - Vladimir A Pomogaev
- Department of Physics, Tomsk State University, Tomsk, 634050, Russia
- Department of Chemistry and Green-Nano Materials Research Center, College of Natural Sciences, Kyungpook National University 1370 Sankyuk-dong, Buk-gu, Daegu, 702-701, Republic of Korea
| | - Andrey A Buglak
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia
| | - Alexander N Tarnovsky
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Alexei I Kononov
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia.
| |
Collapse
|
13
|
Bag S, Maiti PK. Tuning molecular fluctuation to boost the conductance in DNA based molecular wires. Phys Chem Chem Phys 2019; 21:23514-23520. [PMID: 31617554 DOI: 10.1039/c9cp03589c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na+ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.
Collapse
Affiliation(s)
- Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, India.
| | | |
Collapse
|
14
|
Pathak P, Yao W, Hook KD, Vik R, Winnerdy FR, Brown JQ, Gibb BC, Pursell ZF, Phan AT, Jayawickramarajah J. Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns. J Am Chem Soc 2019; 141:12582-12591. [PMID: 31322869 DOI: 10.1021/jacs.9b03250] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated β-cyclodextrin (PMβCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMβCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.
Collapse
Affiliation(s)
- Pravin Pathak
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Wei Yao
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Katherine Delaney Hook
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Ryan Vik
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Jonathon Quincy Brown
- Department of Biomedical Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Bruce C Gibb
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Janarthanan Jayawickramarajah
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| |
Collapse
|
15
|
Banyasz A, Balanikas E, Martinez-Fernandez L, Baldacchino G, Douki T, Improta R, Markovitsi D. Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and Dynamical Features. J Phys Chem B 2019; 123:4950-4957. [PMID: 31117607 DOI: 10.1021/acs.jpcb.9b02637] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplexes are four-stranded DNA structures playing a key role in many biological functions and are promising for applications in the field of nanoelectronics. Characterizing the generation and fate of radical cations (electron holes) within these systems is important in relation to the DNA oxidative damage and/or conductivity issues. This study focuses on guanine radicals in G-quadruplexes formed by association of four TGGGGT strands in the presence of Na+ cations, (TG4T)4/Na+. Using nanosecond transient spectroscopy with 266 nm excitation, we quantitatively characterize hydrated ejected electrons and three types of guanine radicals. We show that, at an energy lower by 2.7 eV than the guanine ionization potential, one-photon ionization occurs with quantum yield of (3.5 ± 0.5) × 10-3. Deprotonation of the radical cations is completed within 20 μs, leading to the formation of (G-H2)• radicals, following a strongly nonexponential decay pattern. Within 10 ms, the latter undergoes tautomerization to deprotonated (G-H1)• radicals. The dynamics of the various radicals determined for (TG4T)4/Na+, in connection to those reported previously for telomeric G-quadruplexes TEL21/Na+, is correlated with energetic factors computed by quantum chemical methods. The faster deprotonation of radical cations in (TG4T)4/Na+ compared to TEL21/Na+ explains that irradiation of the former does not generate 8-oxodGuo, which is readily detected by high-performance liquid chromatography/mass spectrometry in the case of TEL21/Na+.
Collapse
Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France.,Univ Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , F-69342 Lyon , France
| | | | - Lara Martinez-Fernandez
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France.,Departamento de Química , Universidad Autónoma de Madrid , c/ Francisco Tomás y Valiente 7, Cantoblanco , 28049 Madrid , Spain
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France
| | - Thierry Douki
- Univ. Grenoble-Alpes, CEA, CNRS, SyMMES UMR , 5819 Grenoble , France
| | - Roberto Improta
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France.,Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16 , I-80134 Napoli , Italy
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France
| |
Collapse
|
16
|
Zhang H, Fu H, Shao X, Dehez F, Chipot C, Cai W. Changes in Microenvironment Modulate the B- to A-DNA Transition. J Chem Inf Model 2019; 59:2324-2330. [PMID: 30767527 DOI: 10.1021/acs.jcim.8b00885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
B- to A-DNA transition is known to be sensitive to the macroscopic properties of the solution, such as salt and ethanol concentrations. Microenvironmental effects on DNA conformational transition have been broadly studied. Providing an intuitive picture of how DNA responds to environmental changes is, however, still needed. Analyzing the chemical equilibrium of B-to-A DNA transition at critical concentrations, employing explicit-solvent simulations, is envisioned to help understand such microenvironmental effects. In the present study, free-energy calculations characterizing the B- to A-DNA transition and the distribution of cations were carried out in solvents with different ethanol concentrations. With the addition of ethanol, the most stable structure of DNA changes from the B- to A-form, in agreement with previous experimental observation. In 60% ethanol, a chemical equilibrium is found, showing reversible transition between B- and A-DNA. Analysis of the microenvironment around DNA suggests that with the increase of ethanol concentration, the cations exhibit a significant tendency to move toward the backbone, and mobility of water molecules around the major groove and backbone decreases gradually, leading eventually to a B-to-A transition. The present results provide a free-energy view of DNA microenvironment and of the role of cation motion in the conformational transition.
Collapse
Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China
| | - Haohao Fu
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China
| | - Xueguang Shao
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China.,State Key Laboratory of Medicinal Chemical Biology , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , China
| | - François Dehez
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , Vandoeuvre-lès-Nancy F-54506 , France.,LPCT, UMR 7019 Université de Lorraine CNRS , Vandoeuvre-lès-Nancy F-54500 , France
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , Vandoeuvre-lès-Nancy F-54506 , France.,LPCT, UMR 7019 Université de Lorraine CNRS , Vandoeuvre-lès-Nancy F-54500 , France.,Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , China
| |
Collapse
|
17
|
Martínez‐Fernández L, Banyasz A, Markovitsi D, Improta R. Topology Controls the Electronic Absorption and Delocalization of Electron Holes in Guanine Quadruplexes. Chemistry 2018; 24:15185-15189. [DOI: 10.1002/chem.201803222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/21/2022]
Affiliation(s)
| | - Akos Banyasz
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | | | - Roberto Improta
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
- Istituto di Biostrutture e BioimmaginiCNR Via Mezzocannone 16 80134 Napoli Italy
| |
Collapse
|
18
|
Lewis FD, Young RM, Wasielewski MR. Tracking Photoinduced Charge Separation in DNA: from Start to Finish. Acc Chem Res 2018; 51:1746-1754. [PMID: 30070820 DOI: 10.1021/acs.accounts.8b00090] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The initial studies of the dynamics of photoinduced charge separation conducted in our laboratories 20 years ago found strongly distance-dependent rate constants over short distances but failed to detect intermediates in the transport of positive charge (holes). These observations were consistent with the single-step superexchange or tunneling mechanism that had been observed for numerous donor-bridge-acceptor systems at that time. Subsequent studies found weak distance dependence for hole transport over longer distances in DNA, characteristic of incoherent hopping of either localized or delocalized holes. The introduction of synthetic DNA capped hairpin constructs possessing hole donor and acceptor chromophores (or purine bases) at opposite ends of a base-pair domain made it possible to determine the time required for transit of charge from one chromophore to the other and, in some cases, to distinguish between the transit time and the much faster initial charge injection time. These studies eliminated conventional tunneling as a viable mechanism for charge transport in DNA except at very short donor-acceptor separations; however, they did not establish the presence or nature of intermediates in the charge separation process. Recent studies in our laboratories have succeeded in identifying key intermediates as well as untangling the dynamics and efficiency of the charge separation process from start to finish. The dynamics of the initial charge injection process is dependent upon both its free energy and the stacking of the hole donor chromophore and adjacent purine base. The transport of positive charge (holes) over multiple base pairs in duplex DNA occurs most efficiently via repeating adenine bases, known as A-tracts. The transit time across an A-tract is strongly dependent upon the free energy for hole injection, whereas the efficiency of charge separation depends on the competition between charge delocalization and charge recombination in the contact radical ion pair. The guanine cation radical has been detected both by femtosecond transient absorption and by stimulated Raman spectroscopies when the guanine is located near the chromophore employed for hole injection into an A-tract. Replacement of guanine by its derivative 8-phenylethynylguanine (EG), permits tracking of hole transport across longer poly(purine) sequences as a consequence of the stronger transient absorption and stimulated Raman scattering for EG+• vs G+•. We have recently obtained evidence based on femtosecond transient absorption spectroscopy for the formation of delocalized A-polarons in A-tracts possessing four or more A-T base pairs. Similar methods have been used to track hole transport across less-common DNA structures including diblock and triblock poly(purines), locked nucleic acids, three-way junctions, and G-quadruplexes. Similar methods are have been applied to the study of photoinduced electron transport in DNA.
Collapse
Affiliation(s)
- Frederick D. Lewis
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| |
Collapse
|
19
|
The optical properties of adenine cation in different oligonucleotides: a PCM/TD-DFT study. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2223-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
20
|
Wu J, Meng Z, Lu Y, Shao F. Efficient Long-Range Hole Transport Through G-Quadruplexes. Chemistry 2017; 23:13980-13985. [PMID: 28703459 DOI: 10.1002/chem.201702478] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Indexed: 01/09/2023]
Abstract
DNA offers a means of long-range charge transport for biology and electric nanodevices. Here, a series of tetra-stranded G-quadruplexes were assembled within a dendritic DNA architecture to explore oxidative charge transport (hole transport) through the G-quadruplex. Efficient charge transport was achieved over 28 Å upon UV irradiation. Over a longer G-quadruplex bridge, hole transport was escalated to a higher efficiency, which resulted in a higher yield than that of the optimal duplex DNA for charge transport, that is, the adenine tract. Efficient long-range hole transport suggests tetra-stranded G-quadruplexes, instead of an oxidation hotspot, hold better potential as an electron conduit than duplex DNA.
Collapse
Affiliation(s)
- Jingyuan Wu
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Zhenyu Meng
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Yunpeng Lu
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Fangwei Shao
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| |
Collapse
|
21
|
Fujii T, K. Thazhathveetil A, Yildirim I, Young RM, Wasielewski MR, Schatz GC, Lewis FD. Structure and Dynamics of Electron Injection and Charge Recombination in i-Motif DNA Conjugates. J Phys Chem B 2017; 121:8058-8068. [DOI: 10.1021/acs.jpcb.7b04996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Taiga Fujii
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arun K. Thazhathveetil
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ilyas Yildirim
- Department
of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Ryan M. Young
- Argonne-Northwestern Solar Energy Research (ANSER) Center and Institute for Sustainability and Energy at Northwestern, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Argonne-Northwestern Solar Energy Research (ANSER) Center and Institute for Sustainability and Energy at Northwestern, Evanston, Illinois 60208-3113, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| |
Collapse
|
22
|
Brown KE, Singh APN, Wu YL, Mishra AK, Zhou J, Lewis FD, Young RM, Wasielewski MR. Tracking Hole Transport in DNA Hairpins Using a Phenylethynylguanine Nucleobase. J Am Chem Soc 2017; 139:12084-12092. [DOI: 10.1021/jacs.7b06998] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kristen E. Brown
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arunoday P. N. Singh
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Yi-Lin Wu
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Jiawang Zhou
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| |
Collapse
|
23
|
Banyasz A, Martínez-Fernández L, Balty C, Perron M, Douki T, Improta R, Markovitsi D. Absorption of Low-Energy UV Radiation by Human Telomere G-Quadruplexes Generates Long-Lived Guanine Radical Cations. J Am Chem Soc 2017; 139:10561-10568. [PMID: 28737902 DOI: 10.1021/jacs.7b05931] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Telomeres, which are involved in cell division, carcinogenesis, and aging and constitute important therapeutic targets, are prone to oxidative damage. This propensity has been correlated with the presence of guanine-rich sequences, capable of forming four-stranded DNA structures (G-quadruplexes). Here, we present the first study on oxidative damage of human telomere G-quadruplexes without mediation of external molecules. Our investigation has been performed for G-quadruplexes formed by folding of GGG(TTAGGG)3 single strands in buffered solutions containing Na+ cations (TEL21/Na+). Associating nanosecond time-resolved spectroscopy and quantum mechanical calculations (TD-DFT), it focuses on the primary species, ejected electrons and guanine radicals, generated upon absorption of UV radiation directly by TEL21/Na+. We show that, at 266 nm, corresponding to an energy significantly lower than the guanine ionization potential, the one-photon ionization quantum yield is 4.5 × 10-3. This value is comparable to that of cyclobutane thymine dimers (the major UV-induced lesions) in genomic DNA; the quantum yield of these dimers in TEL21/Na+ is found to be (1.1 ± 0.1) × 10-3. The fate of guanine radicals, generated in equivalent concentration with that of ejected electrons, is followed over 5 orders of magnitude of time. Such a quantitative approach reveals that an important part of radical cation population survives up to a few milliseconds, whereas radical cations produced by chemical oxidants in various DNA systems are known to deprotonate, at most, within a few microseconds. Under the same experimental conditions, neither one-photon ionization nor long-lived radical cations are detected for the telomere repeat TTAGGG in single-stranded configuration, showing that secondary structure plays a key role in these processes. Finally, two types of deprotonated radicals are identified: on the one hand, (G-H2)• radicals, stable at early times, and on the other hand, (G-H1)• radicals, appearing within a few milliseconds and decaying with a time constant of ∼50 ms.
Collapse
Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Lara Martínez-Fernández
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Clémence Balty
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Marion Perron
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Thierry Douki
- CEA, INAC-SyMMES Laboratoire des Lésions des Acides Nucléiques, F-38000 Grenoble, France
| | - Roberto Improta
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France.,Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| |
Collapse
|
24
|
Hensel S, Eckey K, Scharf P, Megger N, Karst U, Müller J. Excess Electron Transfer through DNA Duplexes Comprising a Metal‐Mediated Base Pair. Chemistry 2017; 23:10244-10248. [DOI: 10.1002/chem.201702241] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Susanne Hensel
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Kevin Eckey
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Philipp Scharf
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Nicole Megger
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Uwe Karst
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| |
Collapse
|
25
|
Mishra AK, Harris MA, Young RM, Wasielewski MR, Lewis FD. Dynamics of Charge Injection and Charge Recombination in DNA Mini-Hairpins. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b03084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ashutosh Kumar Mishra
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michelle A. Harris
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| |
Collapse
|