Theoretical Study of the Electronic Spectra of Uracil and Thymine

Lorentzon, Johan; Fuelscher, M. P.; Roos, Bjoern O.

doi:10.1021/ja00141a019

Cited by 174 publications

(221 citation statements)

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“…In the case of thymine, we do not find any appreciable signal perpendicular to the base plane contributing to the peak at 4.54 eV. However, this is consistent with TDDFT 26 and CASPT2 28 calculations, as they indeed report nπ* transitions with extremely small oscillation strengths (1e-4-1e-6), unresolved by us. 67 indicate that it is due to a ππ* transition.…”

Section: Isolated Gas-phase Nucleobasessupporting

confidence: 89%

A TDDFT Study of the Excited States of DNA Bases and Their Assemblies

et al. 2006

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We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchangecorrelation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and π-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.

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Section: Isolated Gas-phase Nucleobasessupporting

confidence: 89%

A TDDFT Study of the Excited States of DNA Bases and Their Assemblies

et al. 2006

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“…Analysis of monomer calculations indicates the accuracy with which TDDFT describes spectral properties: excited-state transition energies, transition dipole directions, and oscillator strengths for 2AP, thymine, cytosine, adenine, and guanine (see figures) are in excellent agreement with experimental measurements (16)(17)(18) and with complete active subspace self-consistent field calculations (19,20). Therefore, 5Ј 2AP-N dimers of these bases were built, and TDDFT calculations done on these ''supermolecules,'' so-called because their electronic properties are neither a sum nor perturbation of monomer properties.…”

supporting

confidence: 55%

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

Jean¹

2000

Proceedings of the National Academy of Sciences

133

121

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2-Aminopurine (2AP) is a fluorescent analog of guanosine and adenosine and has been used to probe nucleic acid structure and dynamics. Its spectral features in nucleic acids have been interpreted phenomenologically, in the absence of a rigorous electronic description of the context-dependence of 2AP fluorescence. Now, by using time-dependent density functional theory, we describe the excited-state properties of 2AP in a B-form dinucleotide stacked with guanosine, adenosine, cytosine, or thymine. Calculations predict that 2AP fluorescence is quenched statically when stacked with purines, because of mixing of the molecular orbitals in the ground state. In contrast, quenching is predicted to be dynamic when 2AP is stacked with pyrimidines, because of formation of a low-lying dark excited state. The different quenching mechanisms will result in different experimentally measured fluorescence lifetimes and quantum yields.T he nucleotide 2-aminopurine (2AP) has been used as a site-specific probe of nucleic acid structure and dynamics (1-11) because it base pairs with cytosine in a wobble configuration (4,5,12) or with thymine in a Watson-Crick geometry (7,11). Thermodynamic measurements of DNAs containing 2AP:C or 2AP:T show that the former pairing is more destabilizing (11,12). Incorporating 2AP into DNA quenches its fluorescence (2, 8, 11), reducing its quantum yield from that of the free nucleoside (0.65 in aqueous solution). This reduction is attributed to stacking interactions with nearest neighbor nucleobases, and, therefore, fluorescence properties of 2AP have been used to probe the equilibrium stacking properties of DNA duplexes containing these mismatched pairs (2,8,10). Although the fluorescence decay of 2AP in solution is single exponential, with a lifetime of Ϸ10 ns, in the context of a DNA molecule, four decay components, from 50 ps to 8 ns, are typically needed to describe its lifetime (2). The short decay time observed for 2AP in a duplex is attributed to the fully stacked state, whereas the longest lifetime comes from unstacked 2AP (2, 7). The distribution of stacked states can be altered by temperature, solvent, flanking bases, and bound protein, and so all of these conditions can be probed by using 2AP fluorescence. Dynamics of stacked bases adjacent to a mutagenic mismatch in DNA (such as 2AP:C and 2AP:T) may be part of the recognition mechanism by replication͞repair enzymes (3, 13), so interpretation of 2AP fluorescence data is critical for describing these environments.To understand the effect of base stacking on fluorescent properties of 2AP, we have used time-dependent density functional theory (TDDFT) (14, 15) to calculate the excited-state properties of 2AP alone and in stacked B-and A-form dinucleotides (dimers). Analysis of monomer calculations indicates the accuracy with which TDDFT describes spectral properties: excited-state transition energies, transition dipole directions, and oscillator strengths for 2AP, thymine, cytosine, adenine, and guanine (see figures) are in excellent agreement w...

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“…According to calculations, both Ura (12,15,40) and Thy (15, 40) have a lowest-energy 1 n * state in the gas phase at the equilibrium ground-state geometry. On the other hand, the 1 n * state of isolated Cyt lies slightly above the 1 * state (22).…”

Section: Discussionmentioning

confidence: 99%

Internal conversion to the electronic ground state occurs via two distinct pathways for pyrimidine bases in aqueous solution

Hare

Crespo‐Hernández

Kohler

2007

Proc. Natl. Acad. Sci. U.S.A.

295

488

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The femtosecond transient absorption technique was used to study the relaxation of excited electronic states created by absorption of 267-nm light in all of the naturally occurring pyrimidine DNA and RNA bases in aqueous solution. The results reveal a surprising bifurcation of the initial excited-state population in <1 ps to two nonradiative decay channels within the manifold of singlet states. The first is the subpicosecond internal conversion channel first characterized in 2000. The second channel involves passage through a dark intermediate state assigned to a lowest-energy 1 n * state. Approximately 10 -50% of all photoexcited pyrimidine bases decay via the 1 n * state, which has a lifetime of 10 -150 ps. Three-to 6-fold-longer lifetimes are seen for pyrimidine nucleotides and nucleosides than for the corresponding free bases, revealing an unprecedented effect of ribosyl substitution on electronic energy relaxation. A small fraction of the 1 n * population is proposed to undergo intersystem crossing to the lowest triplet state in competition with vibrational cooling, explaining the higher triplet yields observed for pyrimidine versus purine bases at room temperature. Some simple correlations exist between yields of the 1 n * state and yields of some pyrimidine photoproducts, but more work is needed before the photochemical consequences of this state can be definitively determined. These findings lead to a dramatically different picture of electronic energy relaxation in single pyrimidine bases with important ramifications for understanding DNA photostability.conical intersection ͉ DNA photophysics ͉ excited-state dynamics

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Theoretical Study of the Electronic Spectra of Uracil and Thymine

Cited by 174 publications

References 0 publications

A TDDFT Study of the Excited States of DNA Bases and Their Assemblies

A TDDFT Study of the Excited States of DNA Bases and Their Assemblies

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

Internal conversion to the electronic ground state occurs via two distinct pathways for pyrimidine bases in aqueous solution

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