Thymine photophysics

Cytosine was the first nucleobase whose radiationless decay was studied with quantum mechanical methods. Nevertheless, its first excited states are not so clearly separated as in uracil and thymine, and this causes complications in the computational studies of the photophysics. So, many computational studies have been reported to elucidate the mechanisms for radiationless decay to the ground state but, not always with the same conclusions. 

The effect of solvation on uracil and thymine photophysics has been studied by Gustavvson and coworkers, who have studied uracil with four explicit water molecules and PCM to study distorted geometries [92,93,149], The conical intersection connecting Si to the ground state that was found in the gas phase is also present in solution. The barrier connecting the Si minimum to the conical intersection is lower in solution, however, causing much shorter lifetimes. So the nanosecond lifetime which is observed in the gas phase is not observed in solution but a picosecond lifetime is observed. 

He Y, Wu C, Kong W (2004) Photophysics of methyl-substituted uracils and thymines and their water complexes in the gas phase. J Phys Chem A 108 943... 

The relevance of the dark state to a biological system in water can be elucidated from studies of hydrated complexes. Through the sequential addition of water molecules to thymine, we can observe the gradual change in photophysics as we build up the solvent environment. 

We present experimental results on photophysical deactivation pathways of uracil and thymine bases in the gas phase and in solvent/solute complexes. After photoexcitation to the S2 state, a bare molecule is tunneled into and trapped in a dark state with a lifetime of tens to hundreds of nanoseconds. The nature of this dark state is most likely a low lying nn state. Solvent molecules affect the decay pathways by increasing IC from the S2 to the dark state and then further to the ground state, or directly from S2 to S0. The lifetimes of the S2 state and the dark state are both decreased with the addition of only one or two water molecules. When more than four water molecules are attached, the photophysics of these hydrated clusters rapidly approaches that in the condensed phase. This model is now confirmed from other gas phase and liquid phase experiments, as well as from theoretical calculations. This result offers a new interpretation on the origin of the photostability of nucleic acid bases. Although we believe photochemical stability is a major natural selective force, the reason that the nucleic acid bases have been chosen is not because of their intrinsic stability. Rather, it is the stability of the overall system, with a significant contribution from the environment, that has allowed the carriers of the genetic code to survive, accumulate, and eventually evolve into life s complicated form. 

Becker RS, Kogan G (1980) Photophysical properties of nucleic acid components. 1. The pyrimidines Thymine, uracil, N,N-dimethyl derivatives, and thymidine. Photochemistry and Photobiology 31 5-13. 

The photophysical behaviour of a series of methylated angelicins has been recorded using flash photochemical techniques. Irradiation of the complex formed between 4,6-dimethyltetrahydrobenzoangelicin and DNA results in the formation of cycloadducts. These arise by addition between the pyrimidine bases, thymine and cytosine and the furan ring of the angelicin. 

A photophysical study of the interaction of 2-amino-4,6-dimethylpyrimidine in p-CD has been carried out. Calculations have been carried out in an examination of the isomerism of methyl urocanate. Density functional theory techniques have been used to study the dimerization of thymine units in DNA. The effects of both low intensity irradiation (254 nm) or laser photolysis at 266 nm on adenosine have been reported. The photoionization of various purine and pyrimidine derivatives can be brought about by 266 nm nanosecond laser photolysis. Irradiation of alloxan in the presence of alkenes with allylic hydrogens affords adducts of 5-hydroxy-5-alkenyl barbituric acid. When the alkene is... 

Asturiol D, Lasorne B, Robb MA, Blancafoit L (2009) Photophysics of the pi.pi and n,pi states of thymine Ms-caspt2 minimum-energy paths and casscf on-the-fly dynamics. J Phys Chem A 113 10211... 

Asturiol, D., Lasorne, B., Robb, M. A., Blancafort, L. (2009). Photophysics of the tttt and n,7T states of thymine MS-CASPT2 minimum energy paths and CASSCF on-the-fly dynamics. The Journal of Physical Chemistry A, 113(38), 10211-10218. doi 10.1021/jp905303g. 

A novel method for improving the conductivity of DNA involves close association or even incorporation of divalent metal ions such as Zn, Ni, and Co into the hehx at pH>8.5 to form metallated DNA (M-DNA). Other divalent metals such as Mg + and Ca " do not form M-DNA. In photophysical studies using ds-DNA where one strand is labeled with a fluorescein fluorophore and the complementary strand carries a rhodamine quencher, the fluorescein fluorescence is quenched only under conditions where M-DNA forms. M-DNA is an efficient conductor of electrons over distances as long as 500 basepairs and possibly as long as several micrometers. It was proposed that in M-DNA the Zn cations replace the imino protons of every thymine and guanine in addition to saturating the backbone phosphates as do other cations such as Mg (Scheme 6). Importantly, M-DNA... 

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