High‐Energy Long‐Lived Excited States in DNA Double Strands

Vayá, Ignacio; Miannay, François-Alexandre; Gustavsson, T.; Markovitsi, Dimitra

doi:10.1002/cphc.201000027

Cited by 39 publications

(61 citation statements)

References 26 publications

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“…Low but positive fluorescence anisotropy (0.02) was also found for the peculiar emission band dominating the fluorescence spectrum of alternating guanine‐cytosine duplexes, peaking at shorter wavelengths than ππ* fluorescence . This emission band, decaying on the ns time‐scale, is quenched upon transformation of the B‐form to the Z‐form .…”

Section: Redistribution Of the Excitation Energymentioning

confidence: 84%

UV‐inducedDNADamage: The Role of Electronic Excited States

Markovitsi

2015

Photochem & Photobiology

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The knowledge of the fundamental processes induced by the direct absorption of UV radiation by DNA allows extrapolating conclusions drawn from in vitro studies to the in-vivo DNA photoreactivity. In this respect, the characterization of the DNA electronic excited states plays a key role. For a long time, the mechanisms of DNA lesion formation were discussed in terms of generic "singlet" and "triplet" excited state reactivity. However, since the beginning of the 21 st century, both experimental and theoretical studies revealed the existence of "collective" excited states, i.e. excited states delocalized over at least two bases. Two limiting cases are distinguished: Frenkel excitons (delocalized pp* states) and charge-transfer states in which positive and negative charges are located on different bases. The importance of collective excited states in photon absorption (in particular in the UVA spectral domain), the redistribution of the excitation energy within DNA, and the formation of dimeric pyrimidine photoproducts is discussed. The dependence of the behavior of the collective excited states on conformational motions of the nucleic acids is highlighted.

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Section: Redistribution Of the Excitation Energymentioning

confidence: 84%

UV‐inducedDNADamage: The Role of Electronic Excited States

Markovitsi

2015

Photochem & Photobiology

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“…Despite the fact that the studies on mimetic models of the GC base pair clearly pointed out to an active participation of the proton/hydrogen transfer in the photochemistry of the systems, the relevance of base pairing in the excited-state dynamics of the DNA molecule is still uncertain. 85,86,87,88,89,90,91,92,93,94,95,96 Shortened fluorescence lifetimes in alternating DNA duplexes poly(dGdC)·poly(dGdC) relative to the G and C mononucleotides have been measured experimentally by using fluorescence upconversion spectroscopy, 86 indicating that proton/hydrogen transfer could be relevant, as suggested by theoretical calculations. 85 On the other hand, transient absorption measurements have showed ground-state recovery in the related d(GC) 9 ·d(GC) 9 DNA double strand an order of magnitude slower than in the monomeric nucleotides, suggesting excited-state decays driven by the formation of π-stacked excited-state species (or exciplexes) and not via interstrand proton/hydrogen transfer.…”

Section: Introductionmentioning

confidence: 94%

Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

Sauri

Gobbo

Serrano-Pérez

et al. 2012

J. Chem. Theory Comput.

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Proton/hydrogen-transfer processes have been broadly studied in the last fifty years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine-cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair and a new contribution to tautomerism is provided. The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson-Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. In addition, the C-based imino-enol GC tautomer is thermally less stable. A study of the GC base pair is carried out subsequently taking into account the DNA surroundings in the biological environment. The most important stationary points are computed using the quantum mechanics/molecular mechanics (QM/MM) approach, suggesting a similar scenario for the proton/hydrogen-transfer phenomena in vacuo and DNA. Finally, the static model is complemented by ab initio dynamic simulations, which show that vibrations at the hydrogen bonds can indeed originate hydrogen-transfer processes in the GC base pair. The relevance of the present findings for the rationalization of the preservation of the genetic code and mutagenesis is discussed.

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“…The NMR-based structure of the sequence d[T 2 (G 3 T) 4 )] 34 Potassium cations (K + ) were added to the central channel of starting structures in between stacked G-tetrads. The NMR-based structure of the sequence d[T 2 (G 3 T) 4 )] 34 Potassium cations (K + ) were added to the central channel of starting structures in between stacked G-tetrads.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

“…1 -4 However, in DNA oligomers, long-lived states of up to a nanosecond are observed.1 -4 Charge transfer states and excited state delocalization over two of more nucleobases appear to be responsible for excited state decay occurring on picosecond to nanosecond timescales. 4 Sequences that adopt G-quadruplexes structures are found throughout the human genome, including gene promoters, telomeres, and G-rich repeat sequences. In comparison to duplex DNA, not much is known on the nature of excited states of Gquadruplexes, which are known to play important roles in biological systems 14,15 G-quadruplexes are four-stranded nucleic acid structures formed from the association of guanine bases.…”

Section: Introductionmentioning

confidence: 99%

Influence of Base Stacking Geometry on the Nature of Excited States in G-Quadruplexes: A Time-Dependent DFT Study

et al. 2015

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G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K(+) ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads.

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High‐Energy Long‐Lived Excited States in DNA Double Strands

Cited by 39 publications

References 26 publications

UV‐inducedDNADamage: The Role of Electronic Excited States

UV‐inducedDNADamage: The Role of Electronic Excited States

Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

Influence of Base Stacking Geometry on the Nature of Excited States in G-Quadruplexes: A Time-Dependent DFT Study

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