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Anderson RF, Shinde SS, Andrau L, Leung B, Skene C, White JM, Lobachevsky PN, Martin RF. Chemical Repair of Radical Damage to the GC Base Pair by DNA-Bound Bisbenzimidazoles. J Phys Chem B 2024. [PMID: 38686959 DOI: 10.1021/acs.jpcb.4c01069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The migration of an electron-loss center (hole) in calf thymus DNA to bisbenzimidazole ligands bound in the minor groove is followed by pulse radiolysis combined with time-resolved spectrophotometry. The initially observed absorption spectrum upon oxidation of DNA by the selenite radical is consistent with spin on cytosine (C), as the GC• pair neutral radical, followed by the spectra of oxidized ligands. The rate of oxidation of bound ligands increased with an increase in the ratio (r) ligands per base pair from 0.005 to 0.04. Both the rate of ligand oxidation and the estimated range of hole transfer (up to 30 DNA base pairs) decrease with the decrease in one-electron reduction potential between the GC• pair neutral radical of ca. 1.54 V and that of the ligand radicals (E0', 0.90-0.99 V). Linear plots of log of the rate of hole transfer versus r give a common intercept at r = 0 and a free energy change of 12.2 ± 0.3 kcal mol-1, ascribed to the GC• pair neutral radical undergoing a structural change, which is in competition to the observed hole transfer along DNA. The rate of hole transfer to the ligands at distance, R, from the GC• pair radical, k2, is described by the relationship k2 = k0 exp(constant/R), where k0 includes the rate constant for surmounting a small barrier.
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Affiliation(s)
- Robert F Anderson
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Sujata S Shinde
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Laura Andrau
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Brenda Leung
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Colin Skene
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Jonathan M White
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Pavel N Lobachevsky
- Molecular Radiation Biology, Peter MacCallum Cancer Centre, Melbourne 3052, Australia
| | - Roger F Martin
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
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2
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Merrifield JL, Pimentel EB, Peters-Clarke TM, Nesbitt DJ, Coon JJ, Martell JD. DNA-Compatible Copper/TEMPO Oxidation for DNA-Encoded Libraries. Bioconjug Chem 2023; 34:1380-1386. [PMID: 37540561 PMCID: PMC10831869 DOI: 10.1021/acs.bioconjchem.3c00254] [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] [Indexed: 08/06/2023]
Abstract
Aldehydes are important synthons for DNA-encoded library (DEL) construction, but the development of a DNA-compatible method for the oxidation of alcohols to aldehydes remains a significant challenge in the field of DEL chemistry. We report that a copper/TEMPO catalyst system enables the solution-phase DNA-compatible oxidation of DNA-linked primary activated alcohols to aldehydes. The semiaqueous, room-temperature reaction conditions afford oxidation of benzylic, heterobenzylic, and allylic alcohols in high yield, with DNA compatibility verified by mass spectrometry, qPCR, Sanger sequencing, and ligation assays. Subsequent transformations of the resulting aldehydes demonstrate the potential of this method for robust library diversification.
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Affiliation(s)
- Justice L. Merrifield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Edward B. Pimentel
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Daniel J. Nesbitt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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3
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Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases. Molecules 2022; 27:molecules27217408. [DOI: 10.3390/molecules27217408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.
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Paik D, Lee H, Kim H, Choi JM. Thermodynamics of π–π Interactions of Benzene and Phenol in Water. Int J Mol Sci 2022; 23:ijms23179811. [PMID: 36077201 PMCID: PMC9456204 DOI: 10.3390/ijms23179811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The π–π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π–π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy–entropy compensation. Our comprehensive computational study of the solvation effect on π–π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.
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Affiliation(s)
- Dooam Paik
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hankyul Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Correspondence: (H.K.); (J.-M.C.)
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
- Correspondence: (H.K.); (J.-M.C.)
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5
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Bonesi SM, Protti S, Capucciati A, Fagnoni M. Photogenerated aryl mesylate and aryl diethyl phosphate radical cations: a time-resolved spectroscopy investigation. NEW J CHEM 2022. [DOI: 10.1039/d2nj01755e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photoinduced electron transfer reaction of selected aryl sulfonates and phosphates with K2S2O8 in a MeCN water (9 : 1) mixture has been investigated by LFP experiments.
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Affiliation(s)
- Sergio M. Bonesi
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V.leTaramelli 12, 27100, Pavia, Italy
- Universidad de Buenos Aires, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires, C1428EGA, Argentina
- CONICET—Universidad de Buenos Aires, Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR), Ciudad Universitaria, Buenos Aires, C1428EGA, Argentina
| | - Stefano Protti
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V.leTaramelli 12, 27100, Pavia, Italy
| | | | - Maurizio Fagnoni
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V.leTaramelli 12, 27100, Pavia, Italy
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6
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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.
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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.)
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7
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Deprotonation Dynamics of Guanine Radical Cations †. Photochem Photobiol 2021; 98:523-531. [PMID: 34653259 DOI: 10.1111/php.13540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
This review is dedicated to guanine radical cations (G+ )· that are precursors to oxidatively generated damage to DNA. (G+ )· are unstable in neutral aqueous solution and tend to lose a proton. The deprotonation process has been studied by time-resolved absorption experiments in which (G+ )· radicals are produced either by an electron abstraction reaction, using an external oxidant, or by low-energy/low-intensity photoionization of DNA. Both the position of the released proton and the dynamics of the process depend on the secondary DNA structure. While deprotonation in duplex DNA leads to (G-H1)· radicals, in guanine quadruplexes the (G-H2)· analogs are observed. Deprotonation in monomeric guanosine proceeds with a time constant of ˜60 ns; in genomic DNA, it is completed within 2 µs; and in guanine quadruplexes, it spans from at least 30 ns to over 50 µs. Such a deprotonation dynamics in four-stranded structures, extended over more than three decades of times, is correlated with the anisotropic structure of DNA and the mobility of its hydration shell. In this case, commonly used second-order reaction models are inappropriate for its description.
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Affiliation(s)
| | - Akos Banyasz
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France.,Univ Lyon, ENS de Lyon, CNRS, UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, Lyon, F-69342, France
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France
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8
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Mandal S, Das P. Visible light-induced charge injection and migration in self-assembled carbon dot-DNA-carbon dot nano-dumbbell obtained through controlled stoichiometric conjugation. NANOSCALE 2021; 13:14147-14155. [PMID: 34477696 DOI: 10.1039/d1nr01689j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of carbon dots (CDs) for photonic conversion to charged states, together with the ability of DNA to transport such charge for extensive charge separation, offers an opportunity to control directionality of migration for photo-induced radical cations in CD-DNA based nano-assemblies. This is achieved through engineering the reaction valency of CDs whereby one CD is covalently conjugated with one ssDNA strand. Subsequently, a CD-DNA-CD nano-dumbbell architecture was created through hybridization mediated self-assembly. The time and intensity-dependent transduction of visible light photonic energy to chemical potential in DNA was achieved through irradiation of 1,4-diaminoathraquinone and glyoxal derived CD with 100 W tungsten source and natural sunlight. Following charge injection by CD, the radical cation migration in DNA was perceived through trapping of the hole in repeated GG steps in the DNA. Overall, a breakthrough in visible-light-induced charge transfer by CD into DNA was achieved, potentially applicable to optobioelectronics.
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Affiliation(s)
- Saptarshi Mandal
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
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9
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Akhtar A, Rashid U, Seth C, Kumar S, Broekmann P, Kaliginedi V. Modulating the charge transport in metal│molecule│metal junctions via electrochemical gating. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Wang LL, Wang HH, Wang H, Liu HY. Photoinduced Electron Transfer between DNA and Water-Soluble Porphyrins. J Phys Chem B 2021; 125:5683-5693. [PMID: 34042460 DOI: 10.1021/acs.jpcb.0c09335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photophysical properties of five kinds of porphyrins (H2TMPyP, ZnTMPyP, PdTMPyP, H2TPPS, and ZnTPPS) complexed with model DNAs (ctDNA and dGMP) have been investigated using steady-state absorption, circular dichroism (CD), and femtosecond transient absorption spectroscopy. Upon addition of ctDNA (or dGMP), larger hypochromism and red shifts are observed for H2TMPyP and PdTMPyP compared to the other samples. The steady-state measurements have suggested that the binding modes of H2TMPyP-ctDNA and PdTMPyP-ctDNA are partial intercalation and full intercalation, respectively, while ZnTMPyP-ctDNA shows outside groove binding. No significant interaction was observed between both H2TPPS and ZnTPPS with two kinds of DNA. Upon excitation of the porphyrins into the higher excited state S2 (Soret band), the appearance of the transient absorption from ∼500 to ∼620 nm at about 0.05 ps in H2TMPyP-ctDNA, H2TMPyP-dGMP, and PdTMPyP-dGMP indicates the occurrence of the electron transfer (ET) from guanine to H2TMPyP and PdTMPyP. The forward ET are extremely fast (kf ≥ 1.0 × 1013 s-1), and the backward ET rates are ∼5.6 × 1012 and ∼4.0 × 1012 s-1, respectively. The complexation with DNA may lead to the shorter lifetime of the fluorescence of H2TMPyP and PdTMPyP.
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Affiliation(s)
- Li-Li Wang
- State Key Laboratory of Optoelectronics Materials and Technologies, Sun Yat-Sen University, Guangzhou 510275, China
| | - Hua-Hua Wang
- Department of Chemistry, South China University of Technology, Guangzhou 510641, China
| | - Hui Wang
- State Key Laboratory of Optoelectronics Materials and Technologies, Sun Yat-Sen University, Guangzhou 510275, China
| | - Hai-Yang Liu
- Department of Chemistry, South China University of Technology, Guangzhou 510641, China
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11
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Lorenzo ER, Olshansky JH, Abia DSD, Krzyaniak MD, Young RM, Wasielewski MR. Interaction of Photogenerated Spin Qubit Pairs with a Third Electron Spin in DNA Hairpins. J Am Chem Soc 2021; 143:4625-4632. [PMID: 33735563 DOI: 10.1021/jacs.0c12645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The designing of tunable molecular systems that can host spin qubits is a promising strategy for advancing the development of quantum information science (QIS) applications. Photogenerated radical pairs are good spin qubit pair (SQP) candidates because they can be initialized in a pure quantum state that exhibits relatively long coherence times. DNA is a well-studied molecular system that allows for control of energetics and spatial specificity through careful design and thus serves as a tunable scaffold on which to control multispin interactions. Here, we examine a series of DNA hairpins that use naphthalenediimide (NDI) as the hairpin linker. Photoexcitation of the NDI leads to subnanosecond oxidation of guanine (G) within the duplex or a stilbenediether (Sd) end-cap to give NDI•--G•+ or NDI•--Sd•+ SQPs, respectively. A 2,2,6,6-tetramethylpiperdinyl-1-oxyl (TEMPO) stable radical is covalently attached to the hairpin at varying distances from the SQP spins. While TEMPO has a minimal effect on the SQP formation and decay dynamics, EPR spectroscopy indicates that there are significant spin-spin dipolar interactions between the SQP and TEMPO. We also demonstrate the ability to implement more complex spin manipulations of the NDI•--Sd•+-TEMPO system using pulse-EPR techniques, which is important for developing DNA hairpins for QIS applications.
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Affiliation(s)
- Emmaline R Lorenzo
- Department of Chemistry, Center for Molecular Quantum Transduction, and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Jacob H Olshansky
- Department of Chemistry, Center for Molecular Quantum Transduction, and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Daniel S D Abia
- Department of Chemistry, Center for Molecular Quantum Transduction, and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Matthew D Krzyaniak
- Department of Chemistry, Center for Molecular Quantum Transduction, and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M Young
- Department of Chemistry, Center for Molecular Quantum Transduction, and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R Wasielewski
- Department of Chemistry, Center for Molecular Quantum Transduction, and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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12
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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13
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Ye Z, Du Y, Pan X, Zheng X, Xue J. Electron transfer from guanosine to the lowest triplet excited state of 4-nitroindole through hydrogen-bonded complex. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Abel Y, Vlassiouk I, Lork E, Smirnov S, Talipov MR, Montforts F. Symmetry Effects in Photoinduced Electron Transfer in Chlorin‐Quinone Dyads: Adiabatic Suppression in the Marcus Inverted Region. Chemistry 2020; 26:17120-17127. [PMID: 32628802 PMCID: PMC7839475 DOI: 10.1002/chem.202002736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Indexed: 11/18/2022]
Abstract
In donor–acceptor dyads undergoing photoinduced electron transfer (PET), a direction or pathway for electron movement is usually dictated by the redox properties and the separation distance between the donor and acceptor subunits, while the effect of symmetry is less recognized. We have designed and synthesized two isomeric donor–acceptor assemblies in which electronic coupling between donor and acceptor is altered by the orbital symmetry control with the reorganization energy and charge transfer exothermicity being kept unchanged. Analysis of the optical absorption and luminescence spectra, supported by the DFT and TD‐DFT calculations, showed that PET in these assemblies corresponds to the Marcus inverted region (MIR) and has larger rate for isomer with weaker electronic coupling. This surprising observation provides the first experimental evidence for theoretically predicted adiabatic suppression of PET in MIR, which unambiguously controlled solely by symmetry.
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Affiliation(s)
- Yvonne Abel
- Institut für Organische und Analytische Chemie FB2 Universität Bremen Leobener Straße NW2/C 28359 Bremen Germany
| | - Ivan Vlassiouk
- Oak Ridge National Laboratory Oak Ridge Tennesee 37831 USA
| | - Enno Lork
- Institut für Anorganische Chemie und Kristallographie FB2 Universität Bremen Leobener Straße NW2/C 28359 Bremen Germany
| | - Sergei Smirnov
- Department of Chemistry and Biochemistry New Mexico State University Las Cruces New Mexico 88003 USA
| | - Marat R. Talipov
- Department of Chemistry and Biochemistry New Mexico State University Las Cruces New Mexico 88003 USA
| | - Franz‐Peter Montforts
- Institut für Organische und Analytische Chemie FB2 Universität Bremen Leobener Straße NW2/C 28359 Bremen Germany
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15
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Benitz A, Thomas MB, Silva I, Nesterov VN, Verbeck GF, D'Souza F. Photoinduced Electron Transfer in Axially Coordinated Supramolecular Zinc Tetrapyrrole Bis(styryl)BODIPY Donor‐Acceptor Conjugates. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alejandro Benitz
- Department of Chemistry University of North Texas 1155 Union Circle, #305070 Denton TX 76203–5017 USA
| | - Michael B. Thomas
- Department of Chemistry University of North Texas 1155 Union Circle, #305070 Denton TX 76203–5017 USA
| | - Imesha Silva
- Department of Chemistry University of North Texas 1155 Union Circle, #305070 Denton TX 76203–5017 USA
| | - Vladimir N. Nesterov
- Department of Chemistry University of North Texas 1155 Union Circle, #305070 Denton TX 76203–5017 USA
| | - Guido F. Verbeck
- Department of Chemistry University of North Texas 1155 Union Circle, #305070 Denton TX 76203–5017 USA
| | - Francis D'Souza
- Department of Chemistry University of North Texas 1155 Union Circle, #305070 Denton TX 76203–5017 USA
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16
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Zhou X, Pu H, Sun DW. DNA functionalized metal and metal oxide nanoparticles: principles and recent advances in food safety detection. Crit Rev Food Sci Nutr 2020; 61:2277-2296. [PMID: 32897734 DOI: 10.1080/10408398.2020.1809343] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The frequent occurrence of food safety incidents has given rise to unprecedented concern about food contamination issues for both consumers and the industry. Various contaminations in food pose serious threats to food safety and human health. Many detection methods were studied to address the challenge. Recently, biosensors relying on deoxyribonucleic acid (DNA)-functionalized nanoparticles have been developed as an efficient and effective detection method. In the current review, the strategies for DNA assembly metal and metal oxide nanoparticles are elaborated, recent applications of the sensors based on DNA-functionalized nanoparticles in food contaminant detection are discussed. Pathogenic bacteria, heavy metal ions, mycotoxins, antibiotics, and pesticides are covered as food contaminants. Additionally, limitations and future trends of functionalized nanoparticles-based technology are also presented. The current review indicates that DNA-functionalized metal and metal oxide nanoparticles are a novel nanomaterial with unique biological and physical properties for developing electrochemical, fluorescent, colourimetric and surface-enhanced Raman spectroscopy (SERS) sensors, etc. Compared with conventional detection techniques, DNA-functionalized metal and metal oxide nanoparticles have considerable advantages with high accuracy, high specificity, micro-intelligence, and low cost. Nevertheless, the stability of these sensors and the limitations of real-time detection are still under discussion. Therefore, more tolerant, portable, and rapid DNA sensors should be developed to better the real-time monitoring of harmful contaminants.
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Affiliation(s)
- Xiyi Zhou
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Dublin, Ireland
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17
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Olshansky JH, Zhang J, Krzyaniak MD, Lorenzo ER, Wasielewski MR. Selectively Addressable Photogenerated Spin Qubit Pairs in DNA Hairpins. J Am Chem Soc 2020; 142:3346-3350. [PMID: 32009396 DOI: 10.1021/jacs.9b13398] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Photoinduced electron transfer can produce radical pairs having two quantum entangled electron spins that can act as spin qubits in quantum information applications. Manipulation of these spin qubits requires selective addressing of each spin using microwave pulses. In this work, photogenerated spin qubit pairs are prepared within chromophore-modified DNA hairpins with varying spin qubit distances, and are probed using transient EPR spectroscopy. By performing pulse-EPR measurements on the shortest hairpin, selective addressing of each spin qubit comprising the pair is demonstrated. Furthermore, these spin qubit pairs have coherence times of more than 4 μs, which provides a comfortable time window for performing complex spin manipulations for quantum information applications. The applicability of these DNA-based photogenerated two-qubit systems is discussed in the context of quantum gate operations, specifically the controlled-NOT gate.
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Affiliation(s)
- Jacob H Olshansky
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern , Northwestern University , Evanston Illinois 60208-3113 , United States
| | - Jinyuan Zhang
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern , Northwestern University , Evanston Illinois 60208-3113 , United States
| | - Matthew D Krzyaniak
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern , Northwestern University , Evanston Illinois 60208-3113 , United States
| | - Emmaline R Lorenzo
- 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
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18
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Sun Y, Moe MM, Liu J. Mass spectrometry and computational study of collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation: intra-base-pair proton transfer and hydrogen transfer, non-statistical dissociation, and reaction with a water ligand. Phys Chem Chem Phys 2020; 22:14875-14888. [DOI: 10.1039/d0cp01788d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental and theoretical study is presented on the collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation ([9MG·1MC]˙+) and its monohydrate ([9MG·1MC]˙+·H2O) with Xe and Ar gases.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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19
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Teo RD, Smithwick ER, Migliore A. 2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport. Phys Chem Chem Phys 2019; 21:22869-22878. [PMID: 31599901 PMCID: PMC7050622 DOI: 10.1039/c9cp04805g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The non-biological 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2'F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2'F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs. Inserting these charge-transfer parameters into a kinetic model for charge conduction, we find similar conductive properties for DNA and 2'F-ANA. Moreover, we find that 2'F-ANA's enhanced chemical stability does not correspond to a reduction in the nucleobase π-stack structural flexibility relevant to both electronic couplings and reorganization free energies. Our results promote the use of 2'F-ANA in applications that can be based on charge transport, such as biosensing and chip technology, where its chemical stability and conductivity can advantageously combine.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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20
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Cercola R, Uleanya KO, Dessent CEH. Electron detachment dynamics of the iodide-guanine cluster: does ionization occur from the iodide or from guanine? Mol Phys 2019. [DOI: 10.1080/00268976.2019.1679402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Bortolus M, Ribaudo G, Toffoletti A, Carbonera D, Zagotto G. Photo-induced spin switching in a modified anthraquinone modulated by DNA binding. Photochem Photobiol Sci 2019; 18:2199-2207. [PMID: 30838367 DOI: 10.1039/c8pp00586a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
An anthraquinone modified with a nitroxide radical and able to intercalate into DNA has been synthesized to obtain a molecule the spin state of which can be manipulated by visible light and DNA binding. The doublet ground state of the molecule can be photo-switched to either a strongly coupled spin state (quartet + doublet), when isolated, or to an uncoupled spin state (triplet and doublet), when bound to DNA. The different spin state that is obtained upon photoexcitation depends on the intercalation of the quinonic core into double-stranded DNA which changes the conformation of the molecule, thereby altering the exchange interaction between the excited state localized on the quinonic core and the nitroxide radical. The spin state of the system has been investigated using both continuous-wave and time-resolved EPR spectroscopy.
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Affiliation(s)
- Marco Bortolus
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Giovanni Ribaudo
- Department of Pharmaceutical Sciences, University of Padova, via Marzolo 5, 35131, Padova, Italy
| | - Antonio Toffoletti
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Giuseppe Zagotto
- Department of Pharmaceutical Sciences, University of Padova, via Marzolo 5, 35131, Padova, Italy
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22
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Supermolecules steer electrons down a wrong-way street. Proc Natl Acad Sci U S A 2019; 116:14398-14400. [PMID: 31266894 DOI: 10.1073/pnas.1908872116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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23
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Hosseini M, Roy P, Sissler M, Zirbel CL, Westhof E, Leontis N. How to fold and protect mitochondrial ribosomal RNA with fewer guanines. Nucleic Acids Res 2019; 46:10946-10968. [PMID: 30215760 PMCID: PMC6237812 DOI: 10.1093/nar/gky762] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/06/2018] [Indexed: 01/25/2023] Open
Abstract
Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments and solved 3D ribosome structures from mammalian mitochondria and bacteria, we deduce rules for folding a complex RNA with the remaining guanines shielded from solvent. Almost all conserved guanines in both bacterial and mammalian mitochondrial ribosomal RNA form guanine-specific, local or long-range, RNA–RNA or RNA–protein interactions. Many solvent-exposed guanines conserved in bacteria are replaced in mammalian mitochondria by bases less sensitive to oxidation. New guanines, conserved only in the mitochondrial alignment, are strategically positioned at solvent inaccessible sites to stabilize the ribosomal RNA structure. New mitochondrial proteins substitute for truncated RNA helices, maintain mutual spatial orientations of helices, compensate for lost RNA–RNA interactions, reduce solvent accessibility of bases, and replace guanines conserved in bacteria by forming specific amino acid–RNA interactions.
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Affiliation(s)
- Maryam Hosseini
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Poorna Roy
- Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Marie Sissler
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Neocles Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
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24
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Populations and Dynamics of Guanine Radicals in DNA strands-Direct versus Indirect Generation. Molecules 2019; 24:molecules24132347. [PMID: 31247883 PMCID: PMC6651618 DOI: 10.3390/molecules24132347] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 01/17/2023] Open
Abstract
Guanine radicals, known to be involved in the damage of the genetic code and aging, are studied by nanosecond transient absorption spectroscopy. They are generated in single, double and four-stranded structures (G-quadruplexes) by one and two-photon ionization at 266 nm, corresponding to a photon energy lower than the ionization potential of nucleobases. The quantum yield of the one-photon process determined for telomeric G-quadruplexes (TEL25/Na+) is (5.2 ± 0.3) × 10−3, significantly higher than that found for duplexes containing in their structure GGG and GG sequences, (2.1 ± 0.4) × 10−3. The radical population is quantified in respect of the ejected electrons. Deprotonation of radical cations gives rise to (G-H1)• and (G-H2)• radicals for duplexes and G-quadruplexes, respectively. The lifetimes of deprotonated radicals determined for a given secondary structure strongly depend on the base sequence. The multiscale non-exponential dynamics of these radicals are discussed in terms of inhomogeneity of the reaction space and continuous conformational motions. The deviation from classical kinetic models developed for homogeneous reaction conditions could also be one reason for discrepancies between the results obtained by photoionization and indirect oxidation, involving a bi-molecular reaction between an oxidant and the nucleic acid.
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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.
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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25
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Kaake LG. Towards the Organic Double Heterojunction Solar Cell. CHEM REC 2019; 19:1131-1141. [DOI: 10.1002/tcr.201800180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Loren G. Kaake
- Department of ChemistrySimon Fraser University 8888 University Dr. Burnaby, BC V5A 1S6 Canada
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26
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Abstract
Achieving high-yielding photoinduced charge separation through the π-stacked bases of DNA is a critical requirement for realizing numerous DNA-based technologies. In the current work, we combine two strategies for achieving high-yield charge separation. First, a chromophore with a high driving force for charge injection, naphthalenediimide (NDI), is used because it generates hot carriers that enhance charge-transfer rates. Second, a diblock DNA sequence is used with two or three adenines followed by a series of guanines to implement an energy landscape that accelerates charge separation while retarding charge recombination. The photoinduced dynamics of these NDI diblock oligomers with and without a terminal hole acceptor are probed by femtosecond transient absorption spectroscopy. The measured rate constants for various charge separation and recombination processes are interpreted within the context of a full kinetic model of these systems. We find that the A2 and A3 oligomers achieve similar charge separation yields (as high as 20-25%) for a given length, yet the critical recombination process that determines these yields occurs at different distances from the NDI chromophore and on different time scales. This type of analysis could be used to predict charge separation efficiencies in candidate DNA structures.
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27
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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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28
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Lee YM, Kim S, Ohkubo K, Kim KH, Nam W, Fukuzumi S. Unified Mechanism of Oxygen Atom Transfer and Hydrogen Atom Transfer Reactions with a Triflic Acid-Bound Nonheme Manganese(IV)-Oxo Complex via Outer-Sphere Electron Transfer. J Am Chem Soc 2019; 141:2614-2622. [PMID: 30646680 DOI: 10.1021/jacs.8b12935] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Outer-sphere electron transfer from styrene, thioanisole, and toluene derivatives to a triflic acid (HOTf)-bound nonheme Mn(IV)-oxo complex, [(N4Py)MnIV(O)]2+-(HOTf)2 (N4Py = N, N-bis(2-pyridylmethyl)- N-bis(2-pyridyl)methylamine), has been shown to be the rate-determining step of different types of redox reactions such as epoxidation, sulfoxidation, and hydroxylation of styrene, thioanisole, and toluene derivatives, respectively, by [(N4Py)MnIV(O)]2+-(HOTf)2. The rate constants of HOTf-promoted epoxidation of all styrene derivatives with [(N4Py)MnIV(O)]2+ and electron transfer from electron donors to [(N4Py)MnV(O)]2+ exhibit a remarkably unified correlation with the driving force of outer-sphere electron transfer in light of the Marcus theory of electron transfer. The same electron-transfer driving force dependence is observed in the oxygen atom transfer from [(N4Py)MnIV(O)]2+-(HOTf)2 to thioanisole derivatives as well as in the hydrogen atom transfer from toluene derivatives to [(N4Py)MnIV(O)]2+-(HOTf)2. Thus, mechanisms of oxygen atom transfer (epoxidation and sulfoxidation) reactions of styrene and thioanisole derivatives and hydrogen atom transfer (hydroxylation) reactions of toluene derivatives by [(N4Py)MnIV(O)]2+-(HOTf)2 have been unified for the first time as the same reaction pathway via outer-sphere electron transfer, followed by the fast bond-forming step, which exhibits the singly unified electron-transfer driving force dependence of the rate constants as outer-sphere electron-transfer reactions. In the case of the epoxidation of cis-stilbene by [(N4Py)MnIV(O)]2+-(HOTf)2, the isomerization of cis-stilbene radical cation to trans-stilbene radical cation occurs after outer-sphere electron transfer from cis-stilbene to [(N4Py)MnIV(O)]2+-(HOTf)2 to yield trans-stilbene oxide selectively, which is also taken as evidence for the occurrence of electron transfer in the acid-catalyzed epoxidation.
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Affiliation(s)
- Yong-Min Lee
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea
| | - Surin Kim
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea
| | - Kei Ohkubo
- Institute for Advanced Co-Creation Studies, Open and Transdisciplinary Research Initiatives , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Kyung-Ha Kim
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea.,State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences , Lanzhou 730000 , China
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 03760 , Korea.,Faculty of Science and Engineering , Meijo University , SENTAN, Japan Science and Technology Agency (JST), Nagoya , Aichi 468-0073 , Japan
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29
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Teo RD, Terai K, Migliore A, Beratan DN. Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability. Phys Chem Chem Phys 2018; 20:26063-26067. [PMID: 30191207 PMCID: PMC6202212 DOI: 10.1039/c8cp04816a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The non-biological nucleic acid 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be of use because of its higher chemical stability than DNA in terms of resistance to hydrolysis and nuclease degradation. In order to investigate the charge transfer characteristics of 2'F-ANA, of relevance to applications in nucleic acid-based biosensors and chip technologies, we compare the electronic couplings for hole transfer between stacked nucleobase pairs in DNA and 2'F-ANA by carrying out density functional theory (DFT) calculations on geometries taken from molecular dynamics simulations. We find similar averages and distribution widths of the base-pair couplings in the two systems. On the basis of this result, 2'F-ANA is expected to have charge transfer properties similar to those of DNA, while offering the advantage of enhanced chemical stability. As such, 2'F-ANA may serve as a possible alternative to DNA for use in a broad range of nanobiotechnological applications. Furthermore, we show that the (experimentally observed) enhanced chemical stability resulting from the backbone modifications does not cause reduced fluctuations of the base-pair electronic couplings around the values found for "ideal" B-DNA (with standard step parameter values). Our study also supports the use of a DFT implementation, with the M11 functional, of the wave function overlap method to compute effective electronic couplings in nucleic acid systems.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
| | - Kiriko Terai
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. and Department of Natural Science, College of Liberal Arts, International Christian University, Osawa, Mitaka-shi, Tokyo 181-8585, Japan
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. and Department of Physics, Duke University, Durham, North Carolina 27708, USA and Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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30
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Fagnani DE, Bou Zerdan R, Castellano RK. Synthesis, Optoelectronic Properties, Self-Association, and Base Pairing of Nucleobase-Functionalized Oligothiophenes. J Org Chem 2018; 83:12711-12721. [PMID: 30230836 DOI: 10.1021/acs.joc.8b02138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Device-relevant π-conjugated oligothiophenes with the canonical nucleobases directly embedded into the π-framework have been designed, synthesized, and characterized. These oligomers offer the ability to tune optoelectronic properties via the intimate merging of the nucleobase molecular electronic structure with base-pairing fidelity. Analysis of their optical and electronic properties in a hydrogen-bond-disrupting solvent (DMF) indicates that the nucleobase identity influences the intrinsic electronic properties of the semiconductors. These differences are supported by DFT calculations which demonstrate that the HOMO/LUMO orbitals are distributed differently for each compound. The solubility and competition between self-association and base pairing in a hydrogen-bond-supporting solvent (chloroform) was studied to better understand the oligomer behavior under conditions relevant for downstream solution processing into thin-film devices. These solution studies reveal that in each case base-pairing is preferred to self-aggregation; the relatively weak heteroassociation of 1A-1U (35 ± 5 M-1) should be amenable to facile solution processing and successive hydrogen bond formation in the solid state, while the strong heteroassociation between 1G and 1C (>104 M-1) should enable assemblies to be preformed in solution. These results are expected to enable the synthesis of more complex π-conjugated architectures and facilitate their extension to optoelectronic devices.
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Affiliation(s)
- Danielle E Fagnani
- Department of Chemistry , University of Florida , P.O. Box 117200, Gainesville , Florida 32611 , United States
| | - Raghida Bou Zerdan
- Department of Chemistry , University of Florida , P.O. Box 117200, Gainesville , Florida 32611 , United States
| | - Ronald K Castellano
- Department of Chemistry , University of Florida , P.O. Box 117200, Gainesville , Florida 32611 , United States
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31
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Hammler D, Marx A, Zumbusch A. Fluorescence-Lifetime-Sensitive Probes for Monitoring ATP Cleavage. Chemistry 2018; 24:15329-15335. [PMID: 30070405 DOI: 10.1002/chem.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/14/2022]
Abstract
Adenosine triphosphate (ATP) probes modified with fluorescence dyes that change their fluorescence properties upon cleavage are an interesting tool for monitoring enzymatic ATP turnover. As a readout parameter, fluorescence lifetime is attractive because it is nearly independent of concentration. In our study, we synthesised and investigated fifteen different ATP analogues, in which the fluorophores were attached to the γ-phosphate of ATP. All analogues showed distinctly different fluorescence lifetimes compared to the corresponding values of the free fluorophores. Both increases and decreases in fluorescence lifetime were observed upon attachment to ATP. To shed light on the photophysical processes governing the lifetime changes, we performed photoelectron spectroscopy in air (PESA) to determine HOMO energy levels and time-resolved fluorescence spectroscopy to obtain rate constants. We present evidence that fluorescence quenching in the compounds tested is dynamic and attributed to photoinduced electron transfer (PET), whereas fluorescence lifetime increases are caused by stacking interactions between chromophore and the nucleobase reducing non-radiative relaxation. Finally, we demonstrate that enzymatic cleavage of the ATP analogues presented can be followed by continuous monitoring of fluorescence lifetime changes.
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Affiliation(s)
- Daniel Hammler
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry and Center for Applied Photonics, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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32
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Lang B. Photometrics of ultrafast and fast broadband electronic transient absorption spectroscopy: State of the art. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:093112. [PMID: 30278696 DOI: 10.1063/1.5039457] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
The physical limits of the photometric resolution in broadband electronic transient absorption spectroscopy are discussed together with solutions for how to reach these limits in practice. In the first part, quantitative expressions for the noise contributions to the transient absorption signal are derived and experimentally tested. Experimental approaches described in the literature are discussed and compared on this basis. Guide-lines for designing a setup are established. In the second part, a method for obtaining nearly shot-noise limited kinetics with photometric resolution of the order of 100 μOD in overall measurement times of a few minutes from femtosecond to microsecond time scale is presented. The results are discussed in view of other experiments of step-scan type which are subject to a background or to correlated noise. Finally, detailed information is provided on how to obtain transient absorption spectra where counting statistics are the sole source of noise. A method for how to suppress outliers without introducing bias is discussed. An application example is given to demonstrate the achievable signal-to-noise level and the fast acquisition time.
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Affiliation(s)
- Bernhard Lang
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Genève 4, Switzerland
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33
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Liu Y, Kannegulla A, Wu B, Cheng LJ. Quantum Dot Fullerene-Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection. ACS APPLIED MATERIALS & INTERFACES 2018; 10:18524-18531. [PMID: 29763288 DOI: 10.1021/acsami.8b03552] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Spherical fullerene (C60) can quench the fluorescence of a quantum dot (QD) through energy-transfer and charge-transfer processes, with the quenching efficiency regulated by the number of proximate C60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C60-labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C60-based MBs carried by magnetic nanoparticles. The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance three-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (<10 min) with a small sample volume (1-10 μL). The high signal-to-noise ratio produced by the QD-C60 pairs and magnetic concentration yielded a detection limit of 100 fM (∼106 target DNA copies for a 10 μL analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.
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Affiliation(s)
- Ye Liu
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Akash Kannegulla
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Bo Wu
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Li-Jing Cheng
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
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34
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Capobianco A, Landi A, Peluso A. Modeling DNA oxidation in water. Phys Chem Chem Phys 2018; 19:13571-13578. [PMID: 28513687 DOI: 10.1039/c7cp02029e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel set of hole-site energies and electronic coupling parameters to be used, in the framework of the simplest tight-binding approximation, for predicting DNA hole trapping efficiencies and rates of hole transport in oxidized DNA is proposed. The novel parameters, significantly different from those previously reported in the literature, have been inferred from reliable density functional calculations, including both the sugar-phosphate ionic backbone and the effects of the aqueous environment. It is shown that most of the experimental oxidation free energies of DNA tracts and of oligonucleotides available from photoelectron spectroscopy and voltammetric measurements are reproduced with great accuracy, without the need for introducing sequence dependent parameters.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, I-84084 Fisciano (SA), Italy.
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35
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van Grondelle R. Photoinduced processes in nucleic acids and proteins: concluding remarks. Faraday Discuss 2018; 207:513-521. [PMID: 29564457 DOI: 10.1039/c8fd00049b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light induced charge and energy transport in nucleic acids and proteins is the basis of fundamental biological processes such as photosynthesis, vision, DNA-photostability, DNA-photodamage and photosensing. This article summarises the concluding remarks given at the Faraday Discussions meeting on this topic. The specific themes arising from the meeting that are discussed herein include charge transfer in nucleic acids and proteins, excited state dynamics and topology, vibrations and dynamic disorder, proteins and charge transfer states, nanobiophotonics coupled to biomedical applications and photosynthesis.
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Affiliation(s)
- Rienk van Grondelle
- Faculty of Science, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, The Netherlands
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36
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Sha R, Xiang L, Liu C, Balaeff A, Zhang Y, Zhang P, Li Y, Beratan DN, Tao N, Seeman NC. Charge splitters and charge transport junctions based on guanine quadruplexes. NATURE NANOTECHNOLOGY 2018; 13:316-321. [PMID: 29483600 DOI: 10.1038/s41565-018-0070-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-assemble into multi-ended junctions, and nucleobase stacks can transport charge over long distances. However, nucleobase stacking is often disrupted at junction points, hindering electric charge transport between the two terminals of the junction. Here, we show that a guanine-quadruplex (G4) motif can be used as a connector element for a multi-ended DNA junction. By attaching specific terminal groups to the motif, we demonstrate that charges can enter the structure from one terminal at one end of a three-way G4 motif, and can exit from one of two terminals at the other end with minimal carrier transport attenuation. Moreover, we study four-way G4 junction structures by performing theoretical calculations to assist in the design and optimization of these connectors.
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Affiliation(s)
- Ruojie Sha
- Department of Chemistry, New York University, New York, NY, USA
| | - Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Chaoren Liu
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Alexander Balaeff
- Departments of Chemistry, Duke University, Durham, NC, USA
- Nanoscience Technology Center & Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Yuqi Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Peng Zhang
- Departments of Chemistry, Duke University, Durham, NC, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - David N Beratan
- Departments of Chemistry, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University, Durham, NC, USA.
- Department of Physics, Duke University, Durham, NC, USA.
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, USA.
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37
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Simple G-quadruplex-based 2-aminopurine fluorescence probe for highly sensitive and amplified detection of microRNA-21. Talanta 2018; 178:974-979. [DOI: 10.1016/j.talanta.2017.10.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 01/12/2023]
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38
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Appukutti N, Serpell CJ. High definition polyphosphoesters: between nucleic acids and plastics. Polym Chem 2018. [DOI: 10.1039/c8py00251g] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nucleic acids and synthetic polyphosphoester materials have been distinct fields – this review shows how these areas now comprise a continuum.
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39
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Wang JC, Hill SP, Dilbeck T, Ogunsolu OO, Banerjee T, Hanson K. Multimolecular assemblies on high surface area metal oxides and their role in interfacial energy and electron transfer. Chem Soc Rev 2018; 47:104-148. [DOI: 10.1039/c7cs00565b] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
High surface area metal oxides offer a unique substrate for the assembly of multiple molecular components at an interface.
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Affiliation(s)
- Jamie C. Wang
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Sean P. Hill
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Tristan Dilbeck
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | | | - Tanmay Banerjee
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
- Max Planck Institute for Solid State Research
| | - Kenneth Hanson
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
- Materials Science and Engineering
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40
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Yang Y, Yang W, Su H, Fang W, Chen X. Mechanistic insights into the photogeneration and quenching of guanine radical cation via one-electron oxidation of G-quadruplex DNA. Phys Chem Chem Phys 2018; 20:13598-13606. [DOI: 10.1039/c8cp01718b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Selectivity of activation site for the photogeneration and quenching of guanine radical cation was elucidated by the analysis of the relaxation paths of one-electron oxidation of G-quadruplex DNA.
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Affiliation(s)
- Yumei Yang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Wenjing Yang
- College of Material Science & Engineering
- Taiyuan University of Technology
- People's Republic of China
| | - Hongmei Su
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
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41
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Westphal K, Makurat S, Rak J. The Sequence Dependence of Photoinduced Single Strand Break in 5-Bromo-2′-deoxyuridine Labeled DNA Supports That Electron Transfer Is Responsible for the Damage. J Phys Chem B 2017; 121:9169-9174. [DOI: 10.1021/acs.jpcb.7b07338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kinga Westphal
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Samanta Makurat
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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42
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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
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43
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Inan D, Dubey RK, Westerveld N, Bleeker J, Jager WF, Grozema FC. Substitution Effects on the Photoinduced Charge-Transfer Properties of Novel Perylene-3,4,9,10-tetracarboxylic Acid Derivatives. J Phys Chem A 2017; 121:4633-4644. [PMID: 28558214 PMCID: PMC5483891 DOI: 10.1021/acs.jpca.7b03806] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here the synthesis and photophysical study of a series of electron donor-acceptor molecules, in which electron-donating 4-methoxyphenoxy groups are attached to the 1,7-bay positions of four different perylene tetracarboxylic acid derivatives, namely, perylene tetraesters 1, perylene monoimide diesters 2, perylene bisimides 3, and perylene monobenzimidazole monoimides 4. These perylene derivatives are used because of their increasing order of electron-accepting capability upon moving from 1 to 4. Two additional donor-acceptor molecules are synthesized by linking electron-donating 4-methoxyphenyl groups to the imide position of perylene monoimide diester 2 and perylene bisimide 3. The motivation for this study is to achieve a good control over the photoinduced charge-transfer (CT) process in perylene-based systems by altering the position of electron donors and tuning the electron deficiency of perylene core. A comprehensive study of the photophysical properties of these molecules has shown a highly systematic trend in the magnitude of CT as a function of increased electron deficiency of the perylene core and solvent polarity. Importantly, just by changing the attachment of electron-donating group from "bay" to "imide" position, we are able to block the CT process. This implies that the positioning of the electron donor at the perylene core strongly influences the kinetics of the photoinduced CT process. In these compounds, the CT process is characterized by the quenching of fluorescence and singlet excited-state lifetimes as compared to model compounds bearing non-electron-donating 4-tert-butylphenoxy groups. Transient absorption spectroscopy did not reveal spectra of CT states. This most likely implies that the CT state is not accumulated, because of the faster charge recombination.
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Affiliation(s)
- Damla Inan
- Laboratory of Optoelectronic Materials and ‡Laboratory of Organic Materials & Interfaces Department of Chemical Engineering, Delft University of Technology , Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Rajeev K Dubey
- Laboratory of Optoelectronic Materials and ‡Laboratory of Organic Materials & Interfaces Department of Chemical Engineering, Delft University of Technology , Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Nick Westerveld
- Laboratory of Optoelectronic Materials and ‡Laboratory of Organic Materials & Interfaces Department of Chemical Engineering, Delft University of Technology , Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jorrit Bleeker
- Laboratory of Optoelectronic Materials and ‡Laboratory of Organic Materials & Interfaces Department of Chemical Engineering, Delft University of Technology , Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wolter F Jager
- Laboratory of Optoelectronic Materials and ‡Laboratory of Organic Materials & Interfaces Department of Chemical Engineering, Delft University of Technology , Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ferdinand C Grozema
- Laboratory of Optoelectronic Materials and ‡Laboratory of Organic Materials & Interfaces Department of Chemical Engineering, Delft University of Technology , Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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44
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Abstract
Extensive evidence has shown that long-range charge transport can occur along double helical DNA, but active control (switching) of single-DNA conductance with an external field has not yet been demonstrated. Here we demonstrate conductance switching in DNA by replacing a DNA base with a redox group. By applying an electrochemical (EC) gate voltage to the molecule, we switch the redox group between the oxidized and reduced states, leading to reversible switching of the DNA conductance between two discrete levels. We further show that monitoring the individual conductance switching allows the study of redox reaction kinetics and thermodynamics at single molecular level using DNA as a probe. Our theoretical calculations suggest that the switch is due to the change in the energy level alignment of the redox states relative to the Fermi level of the electrodes. Thanks to its base stacking structure, DNA can behave as an electric wire, but external control of its electronic properties has not been achieved yet. Here, the authors show that DNA conductance can be switched electrochemically when a DNA base is replaced by the redox molecule anthraquinone.
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45
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Abstract
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.
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Affiliation(s)
- Elizabeth O’Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Rebekah M.B. Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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46
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Changenet-Barret P, Gustavsson T, Markovitsi D, Manet I. Ultrafast Electron Transfer in Complexes of Doxorubicin with Human Telomeric G-Quadruplexes and GC Duplexes Probed by Femtosecond Fluorescence Spectroscopy. Chemphyschem 2016; 17:1264-72. [PMID: 26790038 DOI: 10.1002/cphc.201501091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 01/23/2023]
Abstract
Doxorubicin (DOX) is a natural anthracycline widely used in chemotherapy; its combined application as a chemotherapeutic and photodynamic agent has been recently proposed. In this context, understanding the photoinduced properties of DOX complexes with nucleic acids is crucial. Herein, the study of photoinduced electron transfer in DOX-DNA complexes by femtosecond fluorescence spectroscopy is reported. The behaviour of complexes with two model DNA structures, a G-quadruplex (G4) formed by the human telomeric sequence (Tel21) and a d(GC) duplex, is compared. The DOX affinity for these two sequences is similar. Although both 1:1 and 2:1 stoichiometries have been reported for DOX-G4 complexes, only 1:1 complexes form with the duplex. The steady-state absorption indicates a strong binding interaction with the duplex due to drug intercalation between the GC base pairs. In contrast, the interaction of DOX with Tel21 is much weaker and arises from drug binding on the G4 external faces at two independent binding sites. As observed for DOX-d(GC) complexes, fluorescence of the drug in the first binding site of Tel21 exhibits decays within a few picoseconds following a biphasic pattern; this is attributed to the existence of two drug conformations. The fluorescence of the drug in the second binding site of Tel21 shows slower decays within 150 ps. These timescales are consistent with electron transfer from the guanines to the excited drug, as favoured by the lower oxidation potential of the stacked guanines of G4 with respect to those in the duplex.
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Affiliation(s)
- Pascale Changenet-Barret
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France. .,LOB, CNRS, INSERM, Université Paris Saclay, 91128, Palaiseau, France.
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività, CNR, via P. Gobetti 101, 40129, Bologna, Italy.
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47
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Sakamoto R, Wu KH, Matsuoka R, Maeda H, Nishihara H. π-Conjugated bis(terpyridine)metal complex molecular wires. Chem Soc Rev 2016; 44:7698-714. [PMID: 25864838 DOI: 10.1039/c5cs00081e] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bottom-up approaches have gained significant attention recently for the creation of nano-sized, ordered functional structures and materials. Stepwise coordination techniques, in which ligand molecules and metal sources are reacted alternatively, offer several advantages. Coordination bonds are stable, reversible, and self-assembling, and the resultant metal complex motifs may contain functionalities unique to their own characteristics. This review focuses on metal complex wire systems, specifically the bottom-up fabrication of linear and branched bis(terpyridine)metal complex wires on electrode surfaces. This system possesses distinct and characteristic electronic functionalities, intra-wire redox conduction and excellent long-range electron transport ability. This series of comprehensive studies exploited the customizability of bis(terpyridine)metal complex wires, including examining the influence of building blocks. In addition, simple yet effective electron transfer models were established for redox conduction and long-range electron transport. A fabrication technique for an ultra-long bis(terpyridine)metal complex wire is also described, along with its properties and functionalities.
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Affiliation(s)
- Ryota Sakamoto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Kuo-Hui Wu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Ryota Matsuoka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Maeda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroshi Nishihara
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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48
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Kuss-Petermann M, Wenger OS. Electron Transfer Rate Maxima at Large Donor-Acceptor Distances. J Am Chem Soc 2016; 138:1349-58. [PMID: 26800279 DOI: 10.1021/jacs.5b11953] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Because of their low mass, electrons can transfer rapidly over long (>15 Å) distances, but usually reaction rates decrease with increasing donor-acceptor distance. We report here on electron transfer rate maxima at donor-acceptor separations of 30.6 Å, observed for thermal electron transfer between an anthraquinone radical anion and a triarylamine radical cation in three homologous series of rigid-rod-like donor-photosensitizer-acceptor triads with p-xylene bridges. Our experimental observations can be explained by a weak distance dependence of electronic donor-acceptor coupling combined with a strong increase of the (outer-sphere) reorganization energy with increasing distance, as predicted by electron transfer theory more than 30 years ago. The observed effect has important consequences for light-to-chemical energy conversion.
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Affiliation(s)
- Martin Kuss-Petermann
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Oliver S Wenger
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
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49
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Song MX, Li Y, Xu D, Deng RP, Bai FQ, Qin ZK. New exploration towards dinuclear iridium(ii) complexes materials under chlorine-bridged precursor. RSC Adv 2016. [DOI: 10.1039/c6ra10577g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As an important precursor for synthesizing Iridium complex, two similar chlorine-bridged dinuclear complexes, which are bright, were studied by experiment and theory.
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Affiliation(s)
- Ming-Xing Song
- College of Information Technology
- Jilin Normal University
- Siping 136000
- People's Republic of China
| | - Yuan Li
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- China
| | - Duo Xu
- College of Information Technology
- Jilin Normal University
- Siping 136000
- People's Republic of China
| | - Rui-Ping Deng
- State Key Laboratory of Rare Earth Resource Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- People's Republic of China
| | - Fu-Quan Bai
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- China
| | - Zheng-Kun Qin
- College of Information Technology
- Jilin Normal University
- Siping 136000
- People's Republic of China
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50
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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