Thermally induced hopping model for long-range triplet excitation energy transfer in DNA

Blancafort, Lluı́s; Voityuk, Alexander A.

doi:10.1039/c7cp07811k

Cited by 14 publications

(13 citation statements)

References 29 publications

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“…A rather large panel of experimental data are available to assess the decay channels of 3 T leading either to the population of the singlet ground state or to the formation of photodamages, for isolated nucleotides or in single-stranded DNA thymines (21,22). In parallel, several computational studies have considered 3 T embedded in B-DNA, to assess characteristic energies and lifetimes for triplet-triplet energy transfer, either with photosensitizers (23) or along thymine stacks (24,25). In 2011, the characteristic time for triplet migration was estimated at 6.4 ns by semi-empirical quantum chemical methods coupled to classical molecular-dynamics simulations (26).…”

Section: Introductionmentioning

confidence: 99%

The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations^†*

Allahkaram

Monari

Dumont

2021

Photochem & Photobiology

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Among the naturally occurring nucleobases, thymine presents the lowest triplet state, hence it represents a hotspot for energy transfer and photosensitization. In turn, the population of the triplet state may lead to thymine dimerization and hence to the production of toxic DNA lesions and has been the subject of intensive theoretical and experimental investigations. Relying on QM/MM molecular dynamics simulations, we have sought to situate the energy of the lowest triplet state of thymine embedded in a B‐DNA environment. The energy gap varies between 305 and 329 kJ mol−1 when a single thymine is treated at the quantum chemistry level, depending on its position in the model double‐stranded 16‐bp oligonucleotide. The energy of triplet state decreases up to 300 kJ mol−1, due to polarization effects, when we consider coupled stacked nucleobases up to the inclusion of four nucleobases. Our value lies in good agreement with the energy inferred experimentally by Miranda and coworkers (270 kJ mol−1), and our theoretical exploration opens the door to investigations toward other more complex and biologically relevant environments, such as thymines embedded in nucleosome core particles. Our investigations also provide a reference for further studies using semi‐empirical approaches such as density functional‐based tight‐binding, allowing to further rationalize sequence effects.

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Section: Introductionmentioning

confidence: 99%

The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations^†*

Allahkaram

Monari

Dumont

2021

Photochem & Photobiology

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“…The charge migration (CT) toward π-stacked base pairs (BP) is sensitive to its structural and electronic changes. Voityuk [34,35] has shown that the hole migration process between stacked base pairs in ds-DNA can take place between triplet excited states [36][37][38]. From this point, the 8,7-dihydro-8-oxo-2 -deoxyguanosie, which shows a lower ionization energy/potential (6.94 eV [22,39]) than its precursor dG, can easily be oxidized and constitutes an endpoint for cation radical migration, which leads to a) protection of the rest of ds-oligo against oxidation, and b) flagging the lesion for glycosylase movements.…”

Section: Introductionmentioning

confidence: 99%

Clustered DNA Damage: Electronic Properties and Their Influence on Charge Transfer. 7,8-Dihydro-8-Oxo-2′-Deoxyguaosine Versus 5′,8-Cyclo-2′-Deoxyadenosines: A Theoretical Approach

Karwowski

2020

Cells

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Approximately 3 × 1017 DNA damage events take place per hour in the human body. Within clustered DNA lesions, they pose a serious problem for repair proteins, especially for iron–sulfur glycosylases (MutyH), which can recognize them by the electron-transfer process. It has been found that the presence of both 5′,8-cyclo-2′-deoxyadenosine (cdA) diastereomers in the ds-DNA structure, as part of a clustered lesion, can influence vertical radical cation distribution within the proximal part of the double helix, i.e., d[~oxoGcAoxoG~] (7,8-dihydro-8-oxo-2′-deoxyguaosine - oxodG). Here, the influence of cdA, “the simplest tandem lesion”, on the charge transfer through ds-DNA was taken into theoretical consideration at the M062x/6-31+G** level of theory in the aqueous phase. It was shown that the presence of (5′S)- or (5′R)-cdA leads to a slowdown in the hole transfer by one order of magnitude between the neighboring dG→oxodG in comparison to “native” ds-DNA. Therefore, it can be concluded that such clustered lesions can lead to defective damage recognition with a subsequent slowing down of the DNA repair process, giving rise to an increase in mutations. As a result, the unrepaired, oxodG: dA base pair prior to genetic information replication can finally result in GC → TA or AT→CG transversion. This type of mutation is commonly observed in human cancer cells. Moreover, because local multiple damage sites (LMSD) are effectively produced as a result of ionization factors, the presented data in this article might be useful in developing a new scheme of radiotherapy treatment against the background of DNA repair efficiency.

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“…Ab-initio techniques are impractical to treat this problem, and even hybrid methods are challenging: Explicit atomistic calculations at the level of molecular dynamics (for sampling configurations), combined with quantum mechanics/molecular mechanics (QM/MM) methodologies are limited to short sequences and short evolution time [37][38][39][40] . This challenge calls for the development of coarse grained models with perturbative methods [41][42][43][44] , model-system computational schemes 40 , and phenomenological approaches 31,35,36,45 . For example, the fluctuating nuclear environment of DNA can be described by adding noise terms to the static, purely electronic Hamiltonian.…”

Section: B Landauer Büttiker Probe Simulationsmentioning

confidence: 99%

Machine Learning Prediction of DNA Charge Transport

Korol¹,

Segal²

2019

J. Phys. Chem. C

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First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra-and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent electrical conductors is challenging even when adopting coarse-grained models and effective computational schemes that do not explicitly describe atomic dynamics. In this work, we present a machine learning (ML) model that allows the inexpensive prediction of the electrical conductance of millions of long double-stranded DNA (dsDNA) sequences, reducing computational costs by orders of magnitude. The algorithm is trained on short DNA nanojunctions with n = 3 − 7 base pairs. The electrical conductance of the training set is computed with a quantum scattering method, which captures charge-nuclei scattering processes. We demonstrate that the ML method accurately predicts the electrical conductance of varied dsDNA junctions tracing different transport mechanisms: coherent (short-range) quantum tunneling, onresonance (ballistic) transport, and incoherent site-to-site hopping. Furthermore, the ML approach supports physical observations that clusters of nucleotides regulate DNA transport behavior. The input features tested in this work could be used in other ML studies of charge transport in complex polymers, in the search for promising electronic and thermoelectric materials.

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Thermally induced hopping model for long-range triplet excitation energy transfer in DNA

Cited by 14 publications

References 29 publications

The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations^†*

The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations^†*

Clustered DNA Damage: Electronic Properties and Their Influence on Charge Transfer. 7,8-Dihydro-8-Oxo-2′-Deoxyguaosine Versus 5′,8-Cyclo-2′-Deoxyadenosines: A Theoretical Approach

Machine Learning Prediction of DNA Charge Transport

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Thermally induced hopping model for long-range triplet excitation energy transfer in DNA

Cited by 14 publications

References 29 publications

The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations†*

The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations†*

Clustered DNA Damage: Electronic Properties and Their Influence on Charge Transfer. 7,8-Dihydro-8-Oxo-2′-Deoxyguaosine Versus 5′,8-Cyclo-2′-Deoxyadenosines: A Theoretical Approach

Machine Learning Prediction of DNA Charge Transport

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Product

Resources

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The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations^†*

The Behavior of Triplet Thymine in a Model B‐DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations^†*