Depopulation of Highly Excited Singlet States of DNA Model Compounds: Quantum Yields of 193 and 245 nm Photoproducts of Pyrimidine Monomers and Dinucleoside Monophosphates

et al. 2008

Biophysical Journal

118

It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)(18) are fully formed in <1 ps after ultraviolet excitation. The speed and low quantum yield of this reaction suggest that only a small fraction of the conformers of this structurally disordered oligonucleotide are in a position to react at the instant of photon absorption. In this work, we explore the hypothesis that conventional molecular dynamics simulations can be used to predict the yield of cyclobutane pyrimidine dimers in DNA. Conformations obtained from simulations of thymidylyl-(3'-5')-thymidine in various cosolvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine bases and the torsion angle between them. The quantum yield of cyclobutane pyrimidine dimer formation was calculated as the number of dimerizable conformations divided by the total number of conformations. The experimental quantum yields measured in the different solvents were satisfactorily reproduced using physically reasonable values for the two parameters. The mean dimerizable structure computed by averaging all of the dimerizable cis-syn conformations is structurally similar to the actual cis-syn dimer. Compared to the canonical B-form TT step, the most important structural property of a dimerizable conformation is its reduced helical twist angle of 22 degrees.

Section: Experimental Quantum Yieldssupporting

confidence: 91%

Predicting Thymine Dimerization Yields from Molecular Dynamics Simulations

Law

Azadi

et al. 2008

Biophysical Journal

118

“…Understanding these pathways would assist in predicting how low-intensity UV radiation damages DNA and RNA in living organisms. Monophotonic ionization of DNA bases has been confirmed experimentally for 193 nm laser pulses in aqueous solution (7)(8)(9)(10)(11).…”

Section: Introductionmentioning

confidence: 90%

“…A summary of the PI quantum yields is presented for comparison for various DNA and RNA model compounds (7)(8)(9)(10)(11) at excitation wavelengths of 193 and 248 nm in Table 2. The photoejected electron quantum yields obtained by using 193 and 248 nm photons are very similar in magnitude to those obtained at 266 nm.…”

Section: Effect Of the Substituent On The Pi Of Purine And Pyrimidinementioning

confidence: 99%

Photoionization of DNA and RNA Bases, Nucleosides and Nucleotides Through a Combination of One- and Two-photon Pathways upon 266 nm Nanosecond Laser Excitation¶

Arce

2002

Photochem Photobiol

The 266 nm nanosecond laser photolysis of various purine and pyrimidine derivatives results in their photoionization (PI) as one of the primary photochemical pathways. Electron photoejection occurs through a combination of one- and two-photon mechanisms. The PI values depend on the substituents attached to the chromophore of the base. The net PI of the purine bases at 266 nm are of the same order of magnitude (10(-2)) as those of the pyrimidine bases under similar experimental conditions. The monophotonic component is approximately one-third of the net PI yield of the bases. A nonrelaxed singlet excited state intermediate is tentatively proposed for this pathway. It is proposed that this state is significantly stabilized by water solvation, transforming it into a charge transfer to solvent state from which the hydrated electron evolves.

“…A summary of the PI quantum yields is presented for comparison for various DNA and RNA model compounds (7–11) at excitation wavelengths of 193 and 248 nm in Table 2. The photoejected electron quantum yields obtained by using 193 and 248 nm photons are very similar in magnitude to those obtained at 266 nm.…”

Section: Resultsmentioning

confidence: 99%

“…Understanding these pathways would assist in predicting how low‐intensity UV radiation damages DNA and RNA in living organisms. Monophotonic ionization of DNA bases has been confirmed experimentally for 193 nm laser pulses in aqueous solution (7–11).…”

Section: Introductionmentioning

confidence: 99%

Photoionization of DNA and RNA Bases, Nucleosides and Nucleotides Through a Combination of One- and Two-photon Pathways upon 266 nm Nanosecond Laser Excitation¶

Photochemistry and Photobiology

Arce

2007

The 266 nm nanosecond laser photolysis of various purine and pyrimidine derivatives results in their photoionization (PI) as one of the primary photochemical pathways. Electron photoejection occurs through a combination of one‐ and two‐photon mechanisms. The PI values depend on the substituents attached to the chromophore of the base. The net PI of the purine bases at 266 nm are of the same order of magnitude (10−2) as those of the pyrimidine bases under similar experimental conditions. The monophotonic component is approximately one‐third of the net PI yield of the bases. A nonrelaxed singlet excited state intermediate is tentatively proposed for this pathway. It is proposed that this state is significantly stabilized by water solvation, transforming it into a charge transfer to solvent state from which the hydrated electron evolves.