Thymine hydrates

Irradiation of frozen aqueous thymine solutions produces the cis head-to-head (chh) dimer, the high quantum yield (0.5-1.0) being attributed to the preferred orientation of adjacent molecules in the microcrystalline thymine hydrate. The gradual isolation of substrate molecules in the photodimer matrix is associated135 with the appearance and increase in intensity of molecular fluorescence as photodimerization proceeds identical behavior... 

Another type of photochemical reaction involving a pyrimidine base is the addition of a molecule of water across the 5,6 double bond of C to yield a 5,6-dihydro-6-hydroxy derivative called the cytosine hydrate. The quantum yield for the formation of cytosine hydrates in UV-irradiated DNA is greater in single-stranded than in duplex-DNA (45). Hydrates of cytosine, deoxycytidine, CMP, or dCMP are unstable, readily reverting to the parent form by rehydration (45). However, their half-life is dramatically increased in DNA, and cytosine hydrate may be the major nondimer C photoproduct. Cytosine hydrate can undergo deamination and dehydration to yield uracil (1). The hydrate of 5-methylcytosine may undergo deamination to yield 5-thymine hydrate, which can convert to thymine upon dehydration (1). 

Ring-saturated thymine lesions can exist in several stereoisomeric forms which may be energetically distinct depending on their environment. The stereochemistry of thymine glycol (Tg) and thymine hydrate are particularly complex because they have two asymmetric carbon centers. Each asymmetic carbon gives rise to two enantiomers... 

In attempts to isolate the aforementioned irradiated products of thymine derivatives at lower temperature, the photochemical reactions were carried out in frozen aqueous solutions containing either thymine or 1,3-dimethylthymine. The resulting products were not hydrates, but had elementary analyses corresponding to the starting material. Molecular weight determination indicated that the products were dimers, and infrared and ultraviolet spectral data suggested cyclo addition across the 5,6-double bond to form a cyclobutane system... 

From the yields of 5,6-dihydropyrimidine radicals, we predict reduction product yields of 0.04-0.06 pmol/J for 5,6-dihydrouracil and 0.03-0.05 pmol/J for 5,6-dihydro-thymine for B-form DNA hydrated to 9 waters per nucleotide. With respect to oxidation products, we predict strand-break yields —0.10 pmol/J. A very surprising prediction of this model is that the yield of damaged guanine is nil. Half the damage is oxidized sugar products and the other half is reduced pyrimidines. 

Thymine 264.5 7.89 0.43 Slow conversion some hydrate much degrad. 90% conversion to a single dimer a minor product formed... 

The water lattice may be an important element in forming the ordered thymine structure necessary for dimerization, as pointed out by Beukers and Berends.37 Thymine can crystallize from solution as a monohydrate (a real hydrate)38 in whose crystal lattice one thymine is directly above another. The influence of humidity upon dimer yield in dry films may be connected with monohydrate formation, and monohydrate formation in frozen solutions may be the reason for the almost theoretically maximum quantum yields for dimer formation.31 The possible existence of aggregates in frozen aqueous solutions is supported by a tenfold increase in purine phosphorescence at 44°K produced by the presence of 1% ethanol and by a blue shift of excitation and emission spectra.39... 

As concerns the hydration sites of thymine, the interaction energy (its electrostatic component) between thymine and water has been... 

Fig. 17. Hydration sites in thymine.252 Energies in kilocalories per mole. Heavy lines, preferred hydration sites full lines, coplanar arrangement of water and base half-dashed lines, perpendicular arrangement of water with respect to the plane of the base.

The peptide group can be fixed at the ice lattice with p = 0127. Ice-like distances of the H-bond acceptors are in different molecules for example Biotin. Thymine, Triglyceride, 1,4-Quinone etc.141. Hechter gave a model for biologic membranes too142. In the membrane surface Hechter assumes a water double hydrate lamella of 4.9 A thickness in which K+ could be placed, but Na+ would be too big. 

Wardman P, Dennis MF, Everett SA, Patel KB, Stratford MRL, Tracy M (2003) Radicals from one-electron reduction of nitro compounds, aromatic N-oxides and quinones the kinetic basis for hypoxia-selective, bioreductive drugs. Biochem Soc Symp 61 171-194 Warman JM, de Haas MP, Hummel A, van Lith D, VerberneJB, Loman H (1980) A pulse radiolysis conductivity study of frozen aqueous solutions of DNA. Int J Radiat Biol 38 459-459 Warman JM, de Haas MP, Rupprecht A (1996) DNA a molecular wire Chem Phys Lett 249 319-322 Warters RL, Lyons BW (1992) Variation in radiation-induced formation of DNA double-strand breaks as a function of chromatin structure. Radiat Res 130 309-318 Warters RL, Hofer KG, Harris CR, Smith JM (1977) Radionuclide toxicity in cultured mammalian cells Elucidation of the primary site of radiation damage. Curr Top Radiat Res Q 12 389-407 Weiland B, Huttermann J (1998) Free radicals from X-irradiated, dry and hydrated lyophilized DNA as studies by electron spin resonance spectroscopy analysis of spectral components between 77 K and room temperature. Int J Radiat Biol 74 341-358 Weinfeld M, Soderlind K-JM (1991) 32P-Postlabeling detection of radiation-induced DNA-damage identification and estimation of thymine glycols and phosphoglycolate termini. Biochemistry 30 1091-1097... 

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