Intrinsic Lifetimes of the Excited State of DNA and RNA Bases

Kang, Hyuk; Lee, Jun Young; Jung, Boyong; Ko, Yeon Jae; Kim, Seong Keun

doi:10.1021/ja027627x

Cited by 372 publications

(592 citation statements)

References 29 publications

(46 reference statements)

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“…3,4,17 He et al 10,18 observed access to long-lived (23-209 ns) dark states of thymine, methylated thymine, and methylated uracil, as well as a general tendency for longer lifetimes at lower excitation wavelengths (approx. range 290-220 nm) and higher degree of methyl substitution (up to two sites).…”

Section: A Non-dissociative Mpi Of Isolated Uracilmentioning

confidence: 99%

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Barc

Ryszka

Spurrell

et al. 2013

The Journal of Chemical Physics

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Multi-photon ionization (MPI) of the RNA base uracil has been studied in the wavelength range 220–270 nm, coinciding with excitation to the S2(ππ*) state. A fragment ion at m/z = 84 was produced by 2-photon absorption at wavelengths ≤232 nm and assigned to C3H4N2O+ following CO abstraction. This ion has not been observed in alternative dissociative ionization processes (notably electron impact) and its threshold is close to recent calculations of the minimum activation energy for a ring opening conical intersection to a σ(n-π)π* closed shell state. Moreover, the predicted ring opening transition leaves a CO group at one end of the isomer, apparently vulnerable to abstraction. An MPI mass spectrum of uracil-water clusters is presented for the first time and compared with an equivalent dry measurement. Hydration enhances certain fragment ion pathways (particularly C3H3NO+) but represses C3H4N2O+ production. This indicates that hydrogen bonding to water stabilizes uracil with respect to neutral excited-state ring opening.

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Section: A Non-dissociative Mpi Of Isolated Uracilmentioning

confidence: 99%

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Barc

Ryszka

Spurrell

et al. 2013

The Journal of Chemical Physics

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“…The paper also presents equivalent MPI measurements on thymine, for which no analogous ring-opening process has been predicted [9]. A distinctly higher pump energy (5.64 eV, 220 nm) was applied than in the previous MPI studies of thymine (4.34-4.77 eV, 285.7-260 nm) [6,12,13,14,15,16,17], increasing the likelihood of isomeric transitions during radiationless deactivation. Finally, MPI and electron impact ionization (EII) experiments were carried out on uracil-adenine clusters as a step towards better understanding the dissociative ionization pathways of uracil within RNA.…”

Section: Introductionmentioning

confidence: 97%

Dissociative multi-photon ionization of isolated uracil and uracil-adenine complexes

Ryszka

Pandey

Rizk

et al. 2016

International Journal of Mass Spectrometry

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Recent multi-photon ionization (MPI) experiments on uracil revealed a fragment ion at m/z 84 that was proposed as a potential marker for ring opening in the electronically excited neutral molecule. The present MPI measurements on deuterated uracil identify the fragment as C 3 H 4 N 2 O + (uracil + less CO), a plausible dissociative ionization product from the theoretically predicted open-ring isomer. Equivalent measurements on thymine do not reveal an analogous CO loss channel, suggesting greater stability of the excited DNA base. MPI and electron impact ionization experiments have been carried out on uracil-adenine clusters in order to better understand the radiation response of uracil within RNA.Evidence for C 3 H 4 N 2 O + production from multi-photon-ionized uracil-adenine clusters is tentatively attributed to a significant population of π-stacked configurations in the neutral beam. Graphical AbstractHighlights UV multi-photon ionization measurements on deuterated uracil have identified a CO loss pathway that may indicate ring opening in the electronically excited neutral molecule. The first dissociative ionization experiments on uracil-adenine complexes have revealed that the CO loss channel is also accessible in these clusters.Keywords: Uracil; adenine-uracil clusters; fragmentation; multi-photon ionization; electron impact ionization; mass spectrometry Ryszka et al. Int. J. Mass. Spectrom. 396 (2016) 48 2 IntroductionThe dynamics and stabilities of nucleobases following excitation to their bright S 2 (ππ* of the ring-opening crossing seam [9] and the geometry of the predicted isomer indicates likely CO abstraction. Therefore MPI production of this fragment ion was proposed as a potential experimental marker for ring opening in neutral excited uracil, suggesting possibilities for diverse measurements exploring the process in depth (e.g. using coincidence and / or time-resolved methods). The first aim of the present work was to test if the new fragment ion is indeed due to CO loss by studying MPI of deuterated uracil (dominantly C 4 D 4 N 2 O 2 ). These results have the added value of identifying several previously debated fragments from the radical cation, while further evidence to assign specific peaks is provided by high-resolution MPI mass spectra. The paper also presents equivalent MPI measurements on thymine, for which no analogous ring-opening process has been predicted [9]. A distinctly higher pump energy (5.64 eV, 220 nm) was applied than in the previous MPI studies of thymine (4.34-4.77 eV, 285.7-260 nm) [6, 12, 13, 14, 15, 16, 17], increasing the likelihood of isomeric transitions during radiationless deactivation. Finally, MPI and electron impact ionization (EII) experiments were carried out on uracil-adenine clusters as a step towards better understanding the dissociative ionization pathways of uracil within RNA. Whereas several spectroscopic studies have been carried out on adenine-thymine complexes in supersonic beams [18,19,20], to our knowledge no previous experiments on isolated u...

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“…3 The photophysics of isolated cytosine has been the subject of extensive experimental studies with time-resolved spectroscopy. [4][5][6][7][8] Cytosine in the gas phase is of special interest among the nucleic acid bases in various environments, because several tautomeric forms are likely to coexist. Experimental [9][10][11][12][13][14][15][16][17] and theoretical [11][12][13]18 studies have revealed the coexistence of at least three lowest-energy tautomers of isolated cytosine: keto (amino-keto), imino (imino-keto), and enol (amino-enol) forms.…”

Section: Introductionmentioning

confidence: 99%

Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

Nakayama

Harabuchi

Yamazaki

et al. 2013

Phys. Chem. Chem. Phys.

111

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A comprehensive picture of the ultrafast nonradiative decay mechanisms of three cytosine tautomers (amino-keto, imino-keto, and amino-enol forms) is revealed by high-level ab initio potential energy calculations using the multistate (MS) CASPT2 method and also by on-the-fly excited-state molecular dynamics simulations employing the CASSCF method. To obtain a reliable potential energy profile along the deactivation pathways, the MS-CASPT2 method is employed even for the optimization of minimum energy structures in the excited state and conical intersection (CI) structures between the ground and excited states. In the imino (imino-keto) form, we locate a new CI structure involving the twisting of the imino group, and the decay pathway leading to this CI is found to be barrierless, suggesting a remarkably efficient deactivation of imino cytosine. In the keto (amino-keto) form, the MS-CASPT2 calculations exhibit an efficient decay path to the ethylene-like CI involving the twisting of C-C double bond in the six-membered ring, with a barrier of ~0.08 eV from the minimum of the 1 ππ* state. In the enol (amino-enol) form, three types of CIs are identified for the first time. Among them, the ethylene-like CI with a similar molecular structure to the keto form provides the most preferred deactivation pathway of enol cytosine. This pathway exhibits a higher barrier of ~0.22 eV and a higher energy of CI than those of keto cytosine. Nonadiabatic molecular dynamics simulations provide a time-dependent picture of the deactivation processes, including the excited-state lifetime of each tautomer. In particular, the decay time of the imino tautomer is predicted to be only ~100 fs. Our computational results are in remarkably good agreement with the experimental findings in recent femtosecond pump-probe photoionization spectroscopy [J. Am. Chem. Soc. 131, 16939 (2009); J. Phys. Chem. A 115, 8406 (2011)], supporting the coexistence of more than one tautomer in the photophysics of isolated cytosine and that each tautomer exhibits a different excited-state lifetime.1

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Intrinsic Lifetimes of the Excited State of DNA and RNA Bases

Cited by 372 publications

References 29 publications

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Dissociative multi-photon ionization of isolated uracil and uracil-adenine complexes

Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

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