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Vayá I, Gustavsson T, Markovitsi D. High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes. Molecules 2022; 27:molecules27113558. [PMID: 35684495 PMCID: PMC9181881 DOI: 10.3390/molecules27113558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
The publication deals with polymeric pA●pT and oligomeric A20●T20 DNA duplexes whose fluorescence is studied by time-correlated single photon counting. It is shown that their emission on the nanosecond timescale is largely dominated by high-energy components peaking at a wavelength shorter than 305 nm. Because of their anisotropy (0.02) and their sensitivity to base stacking, modulated by the duplex size and the ionic strength of the solution, these components are attributed to mixed ππ*/charge transfer excitons. As high-energy long-lived excited states may be responsible for photochemical reactions, their identification via theoretical studies is an important challenge.
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Affiliation(s)
- Ignacio Vayá
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain;
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Correspondence:
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Martínez-Fernández L, Improta R. Novel adenine/thymine photodimerization channels mapped by PCM/TD-DFT calculations on dApT and TpdA dinucleotides. Photochem Photobiol Sci 2018. [PMID: 28640303 DOI: 10.1039/c7pp00154a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite the biological relevance of AT-rich DNA sequences, the excited state paths associated with the photochemical reactions involving adenine and thymine stacked pairs have never been characterized, and the structure of the most abundant photoproduct in DNA is unknown. PCM/TD-M052X calculations on dApT and TpdA unveil the paths leading to the main photoproduct in TpdA, provide new insights into the reasons why it is not formed in dApT and show the existence of a new photochemical path, which could produce the precursor of the most abundant genomic AT/TA photoproduct. Our calculations confirm that anti/anti conformers are photochemically active and show that the dynamical solvation effects could significantly modulate the reaction yields.
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Affiliation(s)
- Lara Martínez-Fernández
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy
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3
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Role of base arrangements and intermolecular hydrogen bonding in charge-transfer states of thymine-adenine dinucleotide in aqueous solution. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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4
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Vayá I, Brazard J, Huix-Rotllant M, Thazhathveetil AK, Lewis FD, Gustavsson T, Burghardt I, Improta R, Markovitsi D. High-Energy Long-Lived Mixed Frenkel-Charge-Transfer Excitons: From Double Stranded (AT)n to Natural DNA. Chemistry 2016; 22:4904-14. [PMID: 26928984 DOI: 10.1002/chem.201504007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 01/07/2023]
Abstract
The electronic excited states populated upon absorption of UV photons by DNA are extensively studied in relation to the UV-induced damage to the genetic code. Here, we report a new unexpected relaxation pathway in adenine-thymine double-stranded structures (AT)n . Fluorescence measurements on (AT)n hairpins (six and ten base pairs) and duplexes (20 and 2000 base pairs) reveal the existence of an emission band peaking at approximately 320 nm and decaying on the nanosecond time scale. Time-dependent (TD)-DFT calculations, performed for two base pairs and exploring various relaxation pathways, allow the assignment of this emission band to excited states resulting from mixing between Frenkel excitons and adenine-to-thymine charge-transfer states. Emission from such high-energy long-lived mixed (HELM) states is in agreement with their fluorescence anisotropy (0.03), which is lower than that expected for π-π* states (≥0.1). An increase in the size of the system quenches π-π* fluorescence while enhancing HELM fluorescence. The latter process varies linearly with the hypochromism of the absorption spectra, both depending on the coupling between π-π* and charge-transfer states. Subsequently, we identify the common features between the HELM states of (AT)n structures with those reported previously for alternating (GC)n : high emission energy, low fluorescence anisotropy, nanosecond lifetimes, and sensitivity to conformational disorder. These features are also detected for calf thymus DNA in which HELM states could evolve toward reactive π-π* states, giving rise to delayed fluorescence.
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Affiliation(s)
- Ignacio Vayá
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France
| | - Johanna Brazard
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France
| | - Miquel Huix-Rotllant
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France.,Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | | | - Frederick D Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, USA.
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France
| | - Irene Burghardt
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche, Via mezzocannone 16, 80136, Napoli, Italy.
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France.
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5
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Conti I, Nenov A, Höfinger S, Flavio Altavilla S, Rivalta I, Dumont E, Orlandi G, Garavelli M. Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back. Phys Chem Chem Phys 2015; 17:7291-302. [DOI: 10.1039/c4cp05546b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
La and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Siegfried Höfinger
- Zentraler Informatikdienst
- Technische Universität Wien
- 1040 Wien, Austria
- Department of Physics
- Michigan Technological University
| | | | - Ivan Rivalta
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07, France
| | - Elise Dumont
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
- Lyon, France
| | - Giorgio Orlandi
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
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6
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Conti I, Altoè P, Stenta M, Garavelli M, Orlandi G. Adenine deactivation in DNA resolved at the CASPT2//CASSCF/AMBER level. Phys Chem Chem Phys 2010; 12:5016-23. [DOI: 10.1039/b926608a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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de la Harpe K, Crespo-Hernández CE, Kohler B. The excited-state lifetimes in a G x C DNA duplex are nearly independent of helix conformation and base-pairing motif. Chemphyschem 2009; 10:1421-5. [PMID: 19301308 DOI: 10.1002/cphc.200900004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA photophysics: Femtosecond transient absorption experiments reveal that excited states produced by UV light in a duplex DNA oligonucleotide decay at essentially the same rate in B and Z helix conformers (see figure).
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Affiliation(s)
- Kimberly de la Harpe
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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Kwok WM, Ma C, Phillips DL. “Bright” and “Dark” Excited States of an Alternating AT Oligomer Characterized by Femtosecond Broadband Spectroscopy. J Phys Chem B 2009; 113:11527-34. [DOI: 10.1021/jp906265c] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Chensheng Ma
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - David Lee Phillips
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
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Harvey BJ, Perez C, Levitus M. DNA sequence-dependent enhancement of Cy3 fluorescence. Photochem Photobiol Sci 2009; 8:1105-10. [PMID: 19639111 DOI: 10.1039/b905078g] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyanine dyes are extensively used as fluorescent probes in molecular biology, biochemical and biophysical applications. We investigated the fluorescent properties of Cy3 covalently attached to the 5' terminus of DNA oligonucleotides, and demonstrated that its fluorescence efficiency and lifetime depend strongly on DNA sequence. DNA sequence determines the extent and nature of the interactions between the dye and the DNA bases, which are responsible for the unusual enhancement in fluorescence observed for a large number of oligonucleotides. Results are discussed in terms of a photoisomerization mechanism that deactivates the excited state and thus competes with fluorescence. The efficiency of isomerization decreases when Cy3-DNA interactions prevent rotation around the double bonds, resulting in an increase in the lifetime of the singlet excited state. We have shown that the ability of Cy3 to interact with DNA depends on the flexibility of the oligonucleotide and the presence of purines in the chain.
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Affiliation(s)
- Billie Jo Harvey
- Biodesign Institute, Arizona State University, Arizona State University, Tempe, AZ, USA
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Abstract
The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)(18) were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC)(18) at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ~100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.
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Affiliation(s)
| | | | - Bern Kohler
- Corresponding author: e-mail: , Telephone +1-614-688-3944, Fax +1-614-292-1685
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Santoro F, Barone V, Improta R. Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations. Proc Natl Acad Sci U S A 2007; 104:9931-6. [PMID: 17545308 PMCID: PMC1891264 DOI: 10.1073/pnas.0703298104] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thorough study of the excited-state properties of the stacked dimers and trimers of 9-methyladenine in B-DNA conformation has been performed in aqueous solution by using time-dependent density functional calculations and the solvent polarizable continuum model, and results were compared with experimental results on polyadenine oligomers. The effect of base stacking on the absorption and emission spectra is fully reproduced by our calculations. Although light absorption leads to a state (S(B)) delocalized over several nucleobases, excited-state geometry optimization indicates that S(B) subsequently evolves into a state in which the excitation is localized on a single base. Analysis of the excited-state potential energy surfaces shows that S(B) can easily decay into the lowest energy excited state, S(CT), which is a dark excimer produced by intermonomer charge transfer between two stacked bases. The subpicosecond features of the time-resolved experiments are interpreted in terms of ultrafast decay from S(B). After localization, two easy, radiationless decay channels are indeed open for S(B): (i) ground-state recovery, according to the same mechanisms proposed for isolated adenine and/or (ii) decay to S(CT). Our calculations suggest that the slowest part of the excited-state dynamics detected experimentally involves the S(CT) state.
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Affiliation(s)
- F. Santoro
- Istituto per i Processi Chimico–Fisici, Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca del CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - V. Barone
- Dipartimento di Chimica and Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali, Università Federico II, Complesso Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy; and
| | - R. Improta
- Dipartimento di Chimica and Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali, Università Federico II, Complesso Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy; and
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
- To whom correspondence should be addressed. E-mail:
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Daniels M, Hart LP, Ho PS, Ballini JP, Vigny P, Brochon JC. Intrinsic fluorescence of B and Z forms of poly d(G-m5C)·poly d(G-m5C), a synthetic double-stranded DNA: spectra and lifetimes by the maximum entropy method. Photochem Photobiol Sci 2007; 6:883-93. [PMID: 17668119 DOI: 10.1039/b615670c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study has been made of the fluorescence of poly d(G-m5C).poly d(G-m5C), a synthetic double-stranded DNA, in buffered neutral aqueous solution at room temperature, excited by synchrotron radiation at 280 nm and 250 nm and by a frequency-doubled pulse dye laser at 290 nm. Exciting at 280 nm, the B form shows a uni-modal UV spectrum with lambdaf(max) approximately 340 nm. The Z form has in addition a visible emission lambdaf(max) at 450 nm. The spectral positions remain unchanged on exciting at 250 nm but the relative intensities change considerably. Decay profiles have been obtained at 360 nm and 450 nm for both the B and Z forms and have been analyzed by fitting to a pseudo-continuous distribution of 100 (and occasionally 200) exponentials, ranging from 10 ps to 20 ns, by optimizing the 'entropy' of the signal (the method of maximum entropy). We find the mean lifetimes for both wavelengths of emission and for both structural forms fall into three well-separated regions in the ranges indicated tau1 approximately 0.04-0.21 ns, tau2 approximately 0.9-1.26 ns, and tau3 approximately 5.1-6.5 ns. The UV emission, from its spectral position and half-width, correlates with monomeric emission from m5C (and from C for poly d(G-C)). However the lifetime tau1 is approximately 2 orders of magnitude longer than the monomers and points to an involvement of protonated guanosine (GH+, tauf approximately 200 ps) in the overall absorption/emission sequence. In the UV the tau3 emission is predominant, with fractional time-integrated emission approximately 86% for B DNA and approximately 64% for Z. We suggest it results from exciton (stacked) absorption followed by dissociative emission. For Z DNA the visible (450 nm) emission is dominated by a tau3 species (approximately 91%) with a lifetime of 6.5 ns and we suggest it represents a hetero-excimer emission consequent upon absorption by the strongly overlapped base-stacking, which differs from that in B DNA. The weak emission corresponding to tau2 is made more apparent by scanned gated detection of the emission from laser excitation (290 nm) of single-crystal d(m5C-G)3. A central role is attributed to the tight stacking of the bases in the Z form which correlates with enhanced hypochromism at 250 nm vs. 280 nm and with the reversal of the fluorescence intensity ratios UV-visible between these wavelengths.
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Affiliation(s)
- Malcolm Daniels
- Chemistry Department & Radiation Center, Oregon State University, Corvallis, OR 97331, USA
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Colón L, Crespo-Hernández CE, Oyola R, García C, Arce R. Role of Sequence and Conformation on the Photochemistry and the Photophysics of A−T DNA Dimers: An Experimental and Computational Approach. J Phys Chem B 2006; 110:15589-96. [PMID: 16884283 DOI: 10.1021/jp060236a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of base sequence and conformation on the photochemistry and photophysics of thymidylyl (3'-5')-2'-deoxyadenosine sodium salt (TpdA) and 2-deoxyadenylyl (3'-5')-thymidine ammonium salt (dApT) was studied. To this end, nanosecond transient absorption at 266 nm, steady-state irradiation at 254 nm, and quantum chemical calculations were used. The transient absorption spectra show the solvated electron broad band in the visible region for each dinucleotide. In addition, low-intensity absorption bands are observed in the UV region, which are attributed to the deprotonated and protonated neutral radicals of adenine and thymine bases. Photoionization (PI) occurs by one- and two-photon pathways; the latter accounting for approximately 70% of the net PI yield. A diffusion-limited rate constant of 2.0 x 10(10) M(-1) s(-1) was obtained for the reaction of the neutral molecule with the photoejected electron in both sequences. The photodestruction yield, measured from the chromophore loss at 260 nm, decreases in the presence of well-known electron scavengers. This suggests the participation of base radical anions as one of the photodegradation pathways, which is higher in TpdA than in dApT. The intermediacy of a radical ion pair (charge separated state) between the adjacent adenine and thymine bases is proposed in the formation of the [2 + 2] cycloadduct intermediate. The [2 + 2] cycloadduct intermediate is known to be the precursor of the thymine-adenine eight-member ring photoproduct (TA*). Conformational constrains in the radical ion pair are suggested to explain the absence of the TA* photoproduct in dApT. This hypothesis is supported by semiempirical calculations performed on all relevant reactive intermediates proposed to participate in the mechanism of formation of TA*. Altogether, the results show that sequence and conformation profoundly influence the photochemistry and the photophysics of these DNA model systems.
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Affiliation(s)
- Luis Colón
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00931
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Crespo-Hernández CE, Cohen B, Hare PM, Kohler B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chem Rev 2004; 104:1977-2019. [PMID: 15080719 DOI: 10.1021/cr0206770] [Citation(s) in RCA: 962] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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