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Rodríguez-Muñiz GM, Fraga-Timiraos AB, Navarrete-Miguel M, Borrego-Sánchez A, Roca-Sanjuán D, Miranda MA, Lhiaubet-Vallet V. Reductive Photocycloreversion of Cyclobutane Dimers Triggered by Guanines. J Org Chem 2023. [PMID: 37437138 PMCID: PMC10367068 DOI: 10.1021/acs.joc.3c00930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The quest for simple systems achieving the photoreductive splitting of four-membered ring compounds is a matter of interest not only in organic chemistry but also in biochemistry to mimic the activity of DNA photorepair enzymes. In this context, 8-oxoguanine, the main oxidatively generated lesion of guanine, has been shown to act as an intrinsic photoreductant by transferring an electron to bipyrimidine lesions and provoking their cycloreversion. But, in spite of appropriate photoredox properties, the capacity of guanine to repair cyclobutane pyrimidine dimer is not clearly established. Here, dyads containing the cyclobutane thymine dimer and guanine or 8-oxoguanine are synthesized, and their photoreactivities are compared. In both cases, the splitting of the ring takes place, leading to the formation of thymine, with a quantum yield 3.5 times lower than that for the guanine derivative. This result is in agreement with the more favored thermodynamics determined for the oxidized lesion. In addition, quantum chemistry calculations and molecular dynamics simulations are carried out to rationalize the crucial aspects of the overall cyclobutane thymine dimer photoreductive repair triggered by the nucleobase and its main lesion.
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Affiliation(s)
- Gemma M Rodríguez-Muñiz
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
| | - Ana B Fraga-Timiraos
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
| | - Miriam Navarrete-Miguel
- Instituto de Ciencia Molecular, Universitat de València, P.O.Box 22085, 46071 València, Spain
| | - Ana Borrego-Sánchez
- Instituto de Ciencia Molecular, Universitat de València, P.O.Box 22085, 46071 València, Spain
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P.O.Box 22085, 46071 València, Spain
| | - Miguel A Miranda
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
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Kochman MA, Bil A, Miller RJD. Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP). J Phys Chem A 2017; 121:8267-8279. [PMID: 28984456 DOI: 10.1021/acs.jpca.7b08334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzopyridopyrimidine (BPP) is a fluorescent nucleobase analogue capable of forming base pairs with adenine (A) and guanine (G) at different sites. When incorporated into oligodeoxynucleotides, it is capable of differentiating between the two purine nucleobases by virtue of the fact that its fluorescence is largely quenched when it is base-paired to guanine, whereas base-pairing to adenine causes only a slight reduction of the fluorescence quantum yield. In the present article, the photophysics of BPP is investigated through computer simulations. BPP is found to be a good charge acceptor, as demonstrated by its positive and appreciably large electron affinity. The selective quenching process is attributed to charge transfer (CT) from the purine nucleobase, which is predicted to be efficient in the BPP-G base pair, but essentially inoperative in the BPP-A base pair. The CT process owes its high selectivity to a combination of two factors: the ionization potential of guanine is lower than that of adenine, and less obviously, the site occupied by guanine enables a greater stabilization of the CT state through electrostatic interactions than the one occupied by adenine. The case of BPP illustrates that molecular recognition via hydrogen bonding can enhance the selectivity of photoinduced CT processes.
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Affiliation(s)
- Michał A Kochman
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL) , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Andrzej Bil
- Faculty of Chemistry, University of Wrocław , F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL) , Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Chemistry and Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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3
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Wu X, Karsili TNV, Domcke W. Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs. Molecules 2017; 22:molecules22010135. [PMID: 28098833 PMCID: PMC6155867 DOI: 10.3390/molecules22010135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/28/2016] [Accepted: 01/10/2017] [Indexed: 11/16/2022] Open
Abstract
It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G- with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S₁/S₀ conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G- nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G--A and 8-oxo-G--C base pairs are likely too short-lived to be efficient electron-transfer repair agents.
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Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
| | - Tolga N V Karsili
- Department of Chemistry, Temple University, 130 Beury Hall, 1901 N. 13th St., Philadelphia, PA 19122, USA.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
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4
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Beckstead AA, Zhang Y, de Vries MS, Kohler B. Life in the light: nucleic acid photoproperties as a legacy of chemical evolution. Phys Chem Chem Phys 2016; 18:24228-38. [PMID: 27539809 DOI: 10.1039/c6cp04230a] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Photophysical investigations of the canonical nucleobases that make up DNA and RNA during the past 15 years have revealed that excited states formed by the absorption of UV radiation decay with subpicosecond lifetimes (i.e., <10(-12) s). Ultrashort lifetimes are a general property of absorbing sunscreen molecules, suggesting that the nucleobases are molecular survivors of a harsh UV environment. Encoding the genome using photostable building blocks is an elegant solution to the threat of photochemical damage. Ultrafast excited-state deactivation strongly supports the hypothesis that UV radiation played a major role in shaping molecular inventories on the early Earth before the emergence of life and the subsequent development of a protective ozone shield. Here, we review the general physical and chemical principles that underlie the photostability, or "UV hardiness", of modern nucleic acids and discuss the possible implications of these findings for prebiotic chemical evolution. In RNA and DNA strands, much longer-lived excited states are observed, which at first glance appear to increase the risk of photochemistry. It is proposed that the dramatically different photoproperties that emerge from assemblies of photostable building blocks may explain the transition from a world of molecular survival to a world in which energy-rich excited electronic states were eventually tamed for biological purposes such as energy transduction, signaling, and repair of the genetic machinery.
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Affiliation(s)
- Ashley A Beckstead
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400, USA.
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Tuna D, Domcke W. Excited-state deactivation in 8-oxo-deoxyguanosine: comparison between anionic and neutral forms. Phys Chem Chem Phys 2016; 18:947-55. [DOI: 10.1039/c5cp05804j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ab initio explorations of excited-state potential-energy surfaces show that a radiationless deactivation mechanism via intramolecular excited-state proton transfer is available in neutral 8-oxo-deoxyguanosine, whereas it is not available in the anionic form.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
| | - Wolfgang Domcke
- Department of Chemistry
- Technische Universität München
- 85747 Garching
- Germany
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6
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Zhang Y, Dood J, Beckstead AA, Li XB, Nguyen KV, Burrows CJ, Improta R, Kohler B. Photoinduced Electron Transfer in DNA: Charge Shift Dynamics Between 8-Oxo-Guanine Anion and Adenine. J Phys Chem B 2015; 119:7491-502. [PMID: 25660103 DOI: 10.1021/jp511220x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Femtosecond time-resolved IR spectroscopy is used to investigate the excited-state dynamics of a dinucleotide containing an 8-oxoguanine anion at the 5'-end and neutral adenine at the 3'-end. UV excitation of the dinucleotide transfers an electron from deprotonated 8-oxoguanine to its π-stacked neighbor adenine in less than 1 ps, generating a neutral 8-oxoguanine radical and an adenine radical anion. These species are identified by the excellent agreement between the experimental and calculated IR difference spectra. The quantum efficiency of this ultrafast charge shift reaction approaches unity. Back electron transfer from the adenine radical anion to the 8-oxguanine neutral radical occurs in 9 ps, or approximately 6 times faster than between the adenine radical anion and the 8-oxoguanine radical cation (Zhang, Y. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 11612-11617). The large asymmetry in forward and back electron transfer rates is fully rationalized by semiclassical nonadiabatic electron transfer theory. Forward electron transfer is ultrafast because the driving force is nearly equal to the reorganization energy, which is estimated to lie between 1 and 2 eV. Back electron transfer is highly exergonic and takes place much more slowly in the Marcus inverted region.
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Affiliation(s)
- Yuyuan Zhang
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Jordan Dood
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Ashley A Beckstead
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Xi-Bo Li
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Khiem V Nguyen
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Cynthia J Burrows
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Roberto Improta
- §CNR-Consiglio Nazionale delle Ricerche Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, 80136 Napoli, Italy
| | - Bern Kohler
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Barbatti M. Computational reference data for the photochemistry of cyclobutane pyrimidine dimers. Chemphyschem 2014; 15:3342-54. [PMID: 25044616 DOI: 10.1002/cphc.201402302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/19/2023]
Abstract
The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
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8
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Kumar A, Sevilla MD. Excited state proton-coupled electron transfer in 8-oxoG-C and 8-oxoG-A base pairs: a time dependent density functional theory (TD-DFT) study. Photochem Photobiol Sci 2014; 12:1328-40. [PMID: 23478652 DOI: 10.1039/c3pp25430e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a recent experiment, the repair efficiency of DNA thymine cyclobutane dimers (T<>T) on UV excitation of 8-oxoG base paired either to C or A was reported. An electron transfer mechanism from an excited charge transfer state of 8-oxoG-C (or 8-oxoG-A) to T<>T was proposed and 8-oxoG-A was found to be 2-3 times more efficient than 8-oxoG-C in repair of T<>T. Intra base pair proton transfer (PT) in charge transfer (CT) excited states of the base pairs was proposed to quench the excited state and prevent T<>T repair. In this work, we investigate this process with TD-DFT calculations of the excited states of 8-oxoG-C and 8-oxoG-A base pairs in the Watson-Crick and Hoogsteen base pairs using long-range corrected density functional, ωB97XD/6-31G* method. Our gas phase calculations showed that CT excited state ((1)ππ*(CT)) of 8-oxoG-C appears at lower energy than the 8-oxoG-A. For 8-oxoG-C, TD-DFT calculations show the presence of a conical intersection (CI) between the lowest (1)ππ*(PT-CT) excited state and the ground state which likely deactivates the CT excited state via a proton-coupled electron transfer (PCET) mechanism. The (1)ππ*(PT-CT) excited state of 8-oxoG-A base pair lies at higher energy and its crossing with ground state is inhibited because of a high energy gap between (1)ππ*(PT-CT) excited state and ground state. Thus the gas phase calculations suggest the 8-oxoG-A would have longer excited state lifetimes. When the effect of solvation is included using the PCM model, both 8-oxoG-A and 8-oxoG-C show large energy gaps between the ground state and both the excited CT and PT-CT states and suggest little difference would be found between the two base pairs in repair of the T<>T lesion. However, in the FC region the solvent effect is greatly diminished owing to the slow dielectric response time and smaller gaps would be expected.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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9
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Sieradzan I, Marchaj M, Anusiewicz I, Skurski P, Simons J. Prediction of thymine dimer repair by electron transfer from photoexcited 8-aminoguanine or its deprotonated anion. J Phys Chem A 2014; 118:7194-200. [PMID: 24384056 DOI: 10.1021/jp411666a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electronic structure methods are used to estimate differences in reaction barriers for transfer of an electron from singlet ππ* excited 8-aminoguanine (A) or deprotonated 8-aminoguanine anion (A(-)) to a proximal thymine dimer site compared to barriers when ππ* excited 8-oxoguanine (O) or deprotonated 8-oxoguanine (O(-)) serve as the electron donor. It is predicted that the barrier for photoexcited A should be lower than for photoexcited O, and the barrier for photoexcited A(-) should be lower than for photoexcited O(-). Moreover, A, O(-), and A(-) are predicted to have ππ* excited states at energies near where O does, which allows them to be excited by photons low enough in energy to avoid exciting or ionizing any of DNA's bases. The origin of the differences in barriers is suggested to be the lower ionization potential of A compared to O and the lower electron detachment energy of A(-) compared to O(-). Because O and O(-) have been experimentally shown to produce thymine dimer repair, it is proposed that A and A(-) are promising repair agents deserving experimental study.
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Affiliation(s)
- Iwona Sieradzan
- Department of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-308 Gdańsk, Poland
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Abstract
Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany,
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Zhang Y, Dood J, Beckstead A, Chen J, Li XB, Burrows CJ, Lu Z, Matsika S, Kohler B. Ultrafast excited-state dynamics and vibrational cooling of 8-oxo-7,8-dihydro-2'-deoxyguanosine in D2O. J Phys Chem A 2013; 117:12851-7. [PMID: 24215180 DOI: 10.1021/jp4095529] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nguyen and Burrows recently demonstrated that UV-B irradiation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a signature product of oxidatively damaged DNA, can repair cyclobutane pyrimidine dimers in double-stranded DNA (J. Am. Chem. Soc. 2011, 133, 14586 - 14589). In order to test the hypothesis that repair occurs by photoinduced electron transfer, it is critical to determine basic photophysical parameters of 8-oxodG including the excited-state lifetime. Here, femtosecond transient absorption spectroscopy was used to study the ultrafast excited-state dynamics of 8-oxodG with excitation in the UV and probing at visible and mid-IR wavelengths. The excited-state lifetimes of both neutral and basic forms of 8-oxodG in D2O are reported for the first time by monitoring the disappearance of excited-state absorption at 570 nm. The lifetime of the first excited state of the neutral form is 0.9 ± 0.1 ps, or nearly twice as long as that of 2'-deoxyguanosine. The basic form of 8-oxodG exhibits a much longer excited-state lifetime of 43 ± 3 ps. Following ultrafast internal conversion by neutral 8-oxodG, a vibrationally hot ground state is created that dissipates its excess vibrational energy to the solvent on a time scale of 2.4 ± 0.4 ps. Femtosecond time-resolved IR experiments provide additional insights into excited-state dynamics and the vibrational relaxation of several modes in the fingerprint region.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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Marchaj M, Sieradzan I, Anusiewicz I, Skurski P, Simons J. Thymine dimer repair by electron transfer from photo-excited 2′,3′,5′-tri-O-acetyl-8-oxo-7,8-dihydroguanosine or 2′,3′,5′-tri-O-acetyl-ribosyluric acid – a theoretical study. Mol Phys 2013. [DOI: 10.1080/00268976.2013.787152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Marzena Marchaj
- a Department of Chemistry , University of Gdańsk , Gdańsk , Poland
| | - Iwona Sieradzan
- a Department of Chemistry , University of Gdańsk , Gdańsk , Poland
| | - Iwona Anusiewicz
- a Department of Chemistry , University of Gdańsk , Gdańsk , Poland
| | - Piotr Skurski
- a Department of Chemistry , University of Gdańsk , Gdańsk , Poland
- b Chemistry Department and Henry Eyring Center for Theoretical Chemistry , University of Utah , Salt Lake City , UT , USA
| | - Jack Simons
- b Chemistry Department and Henry Eyring Center for Theoretical Chemistry , University of Utah , Salt Lake City , UT , USA
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Nguyen KV, Burrows CJ. Whence flavins? Redox-active ribonucleotides link metabolism and genome repair to the RNA world. Acc Chem Res 2012; 45:2151-9. [PMID: 23054469 DOI: 10.1021/ar300222j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Present-day organisms are under constant environmental stress that damages bases in DNA, leading to mutations. Without DNA repair processes to correct these errors, such damage would be catastrophic. Organisms in all kingdoms have repair processes ranging from direct reversal to base excision and nucleotide excision repair, and the recently characterized giant viruses also include these mechanisms. At what point in the evolution of genomes did active repair mechanisms become critical? In particular, how did early RNA genomes protect themselves from UV photodamage that would have hampered nonenzymatic replication and led to a mutation rate too high to pass on accurate sequence information from one generation to the next? Photolyase is a widespread and phylogenetically ancient enzyme that utilizes longer wavelength light to cleave thymine dimers in DNA produced via photodamage. The protein serves as a binding scaffold but does not contribute to the catalytic chemistry; the action of the dinucleotide cofactor FADH(2) breaks the chemical bonds. This small bit of RNA, hailed as a "fossil of the RNA World," contains the flavin heterocycle, whose redox activity has been harnessed for myriad functions of life from metabolism to DNA repair. In present-day biochemistry, flavin biosynthesis begins with guanosine and proceeds through seven steps catalyzed by protein-based enzymes. This leads to the question of how flavins originally evolved. Did the RNA world include ancestral RNA bases with greater redox activity than G, A, C, and U that were capable of photorepair of uracil dimers? Could those ancestral bases have chemically evolved to the current flavin structure? Or did flavins already exist from prebiotic chemical synthesis? And were they then co-opted as catalysts for repair sometime after metabolism was established? In this Account, we analyze simple derivatives of guanosine and other bases that show two prerequisites for flavin-like photolyase activity: a significantly lowered one-electron reduction potential and a red-shifted adsorption spectrum that facilitates excited-state electron transfer in a spectral window that does not produce cyclobutane pyrimidine dimers. Curiously, the best candidate for a primordial flavin is a base damage product, 8-oxo-7,8-dihydroguanine (8-oxoGua or "OG"). Other redox-active ribonucleotides include 5-hydroxycytidine and 5-hydroxyuridine, which display some of the characteristics of flavins, but might also behave like NADH.
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Affiliation(s)
- Khiem Van Nguyen
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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