Toward the understanding of DNA fluorescence: The singlet excimer of cytosine

Olaso‐González, Gloria; Roca‐Sanjuán, Daniel; Serrano‐Andrés, Luis; Merchán, Manuela

doi:10.1063/1.2408411

Cited by 60 publications

(68 citation statements)

References 25 publications

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“…Calculations aimed at understanding how excited states of nucleobase multimers depend on local structure are just beginning to appear [61][62][63][64], and these will help to resolve these issues. A few studies have even examined cytosine-cytosine base stacks [65,66], but have not yet used geometries from structural biology. Clearly, progress in understanding the electronic structure of these multichromophoric systems will be facilitated by calculations that incorporate realistic structural models.…”

Section: Structural Implicationsmentioning

confidence: 99%

Ultrafast excited-state dynamics of RNA and DNA C tracts

2008

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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 basestacked structure, which may be identical with that of i-motif DNA.

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Section: Structural Implicationsmentioning

confidence: 99%

Ultrafast excited-state dynamics of RNA and DNA C tracts

2008

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“…[39][40][41][42][43][44][45][46] In the present work, we have used the CASPT2 method to compute the vertical electronic spectra of the uracil, thymine, and cytosine · OH adducts and the 5,6-dihydrouracil H-abstraction products. The aim is to provide a unified description of the spectroscopic features of adducts formed in the reaction between the · OH radical and the natural pyrimidine nucleobases and determine the origin of the Vis band measured in transient spectroscopy experiments.…”

Section: The Journal Of Chemical Physics 139 071101 (2013)mentioning

confidence: 99%

Communication: Electronic UV-Vis transient spectra of the ·OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory

Francés‐Monerris

Merchán

Roca‐Sanjuán

2013

The Journal of Chemical Physics

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“…1). To the best of our knowledge, this is the first study on the behavior of excited electronic states performed for stacked multimers of nucleobases by using accurate quantum mechanical methods that include solvent effects (24)(25)(26).…”

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confidence: 99%

Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations

Santoro

Barone²,

Improta

2007

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

124

206

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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 (SB) delocalized over several nucleobases, excited-state geometry optimization indicates that SB 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 SB can easily decay into the lowest energy excited state, SCT, 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 SB. After localization, two easy, radiationless decay channels are indeed open for SB: (i) ground-state recovery, according to the same mechanisms proposed for isolated adenine and/or (ii) decay to SCT. Our calculations suggest that the slowest part of the excited-state dynamics detected experimentally involves the SCT state.nucleic acid ͉ quantum mechanics ͉ spectroscopy ͉ time-dependent phenomena T he absorption of UV light by nucleic acids is a process of primary biophysical interest because it can start a cascade of photochemical reactions leading to base damage and genetic modifications. The photostability of nucleic acids is thus fundamental for the development of life, and its microscopic origin has been the object of several experimental and computational studies (1). Even if a number of important aspects have not yet been convincingly assessed, there is general consensus regarding the mechanisms that explain the photostability of isolated nucleobases. Indeed, time-resolved spectroscopic studies (1) and quantum mechanical calculations (1-11) agree in suggesting the existence of an ultrafast nonradiative pathway between the bright excited state and the ground electronic state for both pyrimidine and purine nucleobases, which can explain their extremely short (Յ1-ps) excited-state lifetimes. However, the excited-state behavior of DNA and nucleobase multimers (the systems of actual interest in vivo) appears much more complex, showing multiexponential decays with very different time constants (12-18). Recent experimental studies on single-stranded polyadenine (polyA) oligomers [(dA) n ] and double-stranded thymine adenine oligonucleotides [(dT) n /(dA) n ] provide deeper insight into the behavior of the multimer excited states and the factors tuning their decay (12-18). In (dA) 18 single-strand and (dA) 18 ⅐(dT) 18 double-strand, a fast initial decay, in the subpicosecond time range, is indeed followed by slower relaxations (lifetimes of Ϸ0.8 and Ϸ126 ps, respectively) (12, 13).Additional time-resolved studies on (dA)...

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Toward the understanding of DNA fluorescence: The singlet excimer of cytosine

Cited by 60 publications

References 25 publications

Ultrafast excited-state dynamics of RNA and DNA C tracts

Ultrafast excited-state dynamics of RNA and DNA C tracts

Communication: Electronic UV-Vis transient spectra of the ·OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory

Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations

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