Detection and chemistry of the triplet state of thymine

Szabo, Arthur G.; Rlddell, W. D.; Yip, R. W.

doi:10.1139/v70-114

Cited by 13 publications

(3 citation statements)

References 4 publications

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“…This process can also be facilitated by the additional stabilization of thymine triplet 3 T due to π-stacking, and the related multichromophoric coupling in the DNA helical structure. Thymine photochemistry has been explored as early as 1960s (11), but the presence of 3 T (12) has triggered renewed attention, notably for delineating the mechanism of triplet-triplet energy transfer with external photosensitizers (13), or with modified nucleobases and oxidative lesions recognized as Trojan Horses (9,14). It has also been shown that the population of 3 T opens rather efficient photochemical channels for dimerization (15,16), even if there is no experimental evidences for the formation of 64-PP mediated by 3 T. The energy of 3 T in a DNA strand has been inferred experimentally by Bosca et al by assessing the energy transfer efficiency of different photosensitizers, such as norfloxacin and its N4'-acetyl derivative, whose energies are precisely known (17).…”

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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“…In solution, for the majority of molecules in the pyrimidine family, excitation is accompanied by an accumulation of lone electrons at C5 and C6 and a marked reduction in bond order. , Dimerization occurs through the generation of a singlet state, followed by intersystem crossing and decay to a triplet state, − from which the dimer is formed. The lifetime of the excited triplet state is much longer than the singlet state and energy is normally dissipated by chemical routes, since there is ample opportunity for molecules to diffuse and collide in solution.…”

Section: Introductionmentioning

confidence: 99%

Light-Induced Surface Wettability of a Tethered DNA Base

2005

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We show that the DNA base thymine and other uracil derivatives, when alkylated with a hydrocarbon chain and assembled at a gold interface, dimerize when subjected to UV irradiation. The process is robust and reversible and is accompanied by a substantial decrease in wettability as well as a marked decrease in acidity constant when the dimer is formed. There is a concerted molecular reorientation that accompanies photodimerization, with the dimer displaying a marked affinity for the gold surface. The spatial requirements for this reorganization are satisfied during dimerization by the reduction in intermolecular distance that occurs when the cyclobutane ring is formed between adjacent bases. The structural changes observed here for a tethered DNA base provide a direct route for exploring reactions, in two dimensions, that are of central interest in biology.

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“…This process can also be facilitated by the additional stabilization of thymine triplet ( 3 T) due to ⇡ stacking, and the related multichromophoric coupling in the DNA helical structure. Thymine photochemistry has been explored as early as 1960s 11 , but the presence of 3 T 12 has triggered renewed attention, notably for delineating the mechanism of triplet-triplet energy transfer with ex-ternal photosensitizers 13 , or with modified nucleobases and oxidative lesions recognized as Trojan Horses 9,14 . It has also been shown that the population of 3 T opens rather e cient photochemical channels for dimerization, and especially for the production of 64-PP.…”

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

Preprint

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Among the natural 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 biological relevant environments, such as thymines embedded in nucleosome core particles. Our investigations also provide a reference for further studies using semiempirical approaches such as density functional based tight binding, allowing to further rationalize sequence effects.

show abstract

Detection and chemistry of the triplet state of thymine

Cited by 13 publications

References 4 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^†*

Light-Induced Surface Wettability of a Tethered DNA Base

The behavior of triplet thymine in a model B-DNA strand. Energetics and spin density localization revealed by ab initio molecular dynamics simulations.

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Detection and chemistry of the triplet state of thymine

Cited by 13 publications

References 4 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†*

Light-Induced Surface Wettability of a Tethered DNA Base

The behavior of triplet thymine in a model B-DNA strand. Energetics and spin density localization revealed by ab initio molecular dynamics simulations.

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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^†*