Thymine reaction

The effect of dithiothreitol (DTT) on DNA radiolysis at cryogenic temperatures was investigated by the EPR technique in order to elucidate its properties as a radioprotector and to establish which DNA radicals can be repaired. The DTT, even at concentrations up to 1 M, does not repair more than 30% of DNA radicals. However, the ability of DTT to donate hydrogen atoms to damaged DNA in frozen aqueous solutions is limited to the allyl radical of thymine [reaction (7)] and guanine radical cation [reaction (8)] ... 

Modified oligonucleotides can be used to cross-link DNA sequences via a reactive group tethered to an oligonucleotide. When irradiated with uv light, psoralens (31) reacts with thymine bases, and the reaction yields a cross-link if the thymine residues are adjacent to each other on opposite strands. Psoralen linked to oligonucleotides have been shown to induce site-specific cross-links in vitro (51). 

In contrast, the photochemistry of uracil, thymine and related bases has a large and detailed literature because most of the adverse effects produced by UV irradiation of tissues seem to result from dimer formation involving adjacent thymine residues in DNA. Three types of reaction are recognizable (i) photohydration of uracil but not thymine (see Section 2.13.2.1.2), (ii) the oxidation of both bases during irradiation and (iii) photodimer formation. 

Irradiation of an aqueous solution of thymine (111 R = Me) in the presence of air produces (irreversibly) at least four products (111 R = CH20H, CHO, CO2H or H), possibly via dithymine peroxide , a linear dimeric molecule (112), The significance of these reactions has been discussed (65MI21300). 

Having a 5-methyl group, thymine is not nitrated or halogenated normally, but with aqueous bromine it does give the dihydropyrimidine (948) (25JBC(64)233) its other reactions parallel those of uracil although its behavior on irradiation is somewhat different (Section 2.13.2.1.4). 

O-isopropylidene derivative (57) must exist in pyridine solution in a conformation which favors anhydro-ring formation rather than elimination. Considerable degradation occurred when the 5-iodo derivative (63) was treated with silver fluoride in pyridine (36). The products, which were isolated in small yield, were identified as thymine and l-[2-(5-methylfuryl)]-thymine (65). This same compound (65) was formed in high yield when the 5 -mesylate 64 was treated with potassium tert-hx Xy -ate in dimethyl sulfoxide (16). The formation of 65 from 63 or 64 clearly involves the rearrangement of an intermediate 2, 4 -diene. In a different approach to the problem of introducing terminal unsaturation into pento-furanoid nucleosides, Robins and co-workers (32,37) have employed mild base catalyzed E2 elimination reactions. Thus, treatment of the 5 -tosylate (59) with potassium tert-butylate in tert-butyl alcohol afforded a high yield of the 4 -ene (60) (37). This reaction may proceed via the 2,5 ... 

Kinoshita, Imoto etal.11 14) synthesized other anionic models, 5 (APVP), CPVP, UPVP, TPVA, HPVA, THPVA, and 6 (AMPPVA), by the polymer reaction of N-eoupled(2-dihydrogenphosphate)-ethylderivatives of nucleic acid bases (or adenosine-5 -phosphate, AMP) with polyvinylaleohol. A, C, U, T, H, and TH denote adenine, cytosine, uracil, thymin, hypoxanthine, and theophylline, respectively. The authors reported the apparent hypochromities of 3 to 16% for many kinds of mixtures of the models and DNA or RNA, as compiled in Table 1. However, for the mixtures APVA + RNA, HPVA + RNA HPVA + DNA, THPVA + RNA, CPVA + DNA and CPVA + RNA, no hypochromicity was detected. 

Nucleic acids are anionic under the neutral conditions. Thus, the syntheses of model compounds of the opposite charge are interesting for the discussion of electrostatic contributions in specific interactions of nucleic acids. We have tried to synthesize cationic models by the Menschutkin reaction of poly-4-vinylpyridine with 9-(2-chlo-roethyl)adenine, l-(2-chloroethyl)thymine, and 7-(2-chloroethyl)theophylline15,16 The obtained polymers are poly l-[2-(adenin-9-yl)ethyl]-4-pyridinioethylene chloride 7(APVP), poly l-[2-(thymin-l-yl)ethyl]-4-pyridinioethylene chloride 8 (TPVP), and poly l-[2-(theophyllin-7-yl)ethyl]-4-pyridiniothylene chloride 9 (THPVP), respectively. 

A 12), 0-(thymin-l-yl)ethyldodecyldimethylamrnonium chloride), 25 (T12), j3-(theophyllin-7-yl)ethyldodecylammonium chloride, 26 (TH12), j3-(adenin-9-yl)-ethyloctadecyldimethylammonium chloride (A 18), and /3-(thymin-l-yl)ethylocta-decyldimethylammonium chloride (T18)47. These model compounds were prepared by the Menschutkin reaction of dodecyldimethyl amine or octadecyldimethylamine with chloroethylated bases. 

N -Fmoc serine benzyl ester 2, which could be prepared as shown or purchased commercially, was smoothly converted to the crystalHne O-methylthiomethyl (MTM) ether 3 in high yield via a Pummerer-Hke reaction using benzoyl peroxide and dimethyl sulfide in acetonitrile [39]. This common intermediate was used to synthesize both 5 and 8 [40]. Both Ogilvie [41] and Tsantrizos [42] had reported that I2 was an effective activator with similar MTM ether substrates. The H promoted nucleosidation reaction between O-MTM ether 3 and bis-silylated thymine 4 produced the nucleoamino acid 5 in 60% isolated yield (100% based on recovered 3). Hydrogenolytic deprotection of the benzyl ester with H2, Pd/C in MeOH gave the thymine-containing nucleoamino acid 6 in quantitative yield. 

Nucleosides containing deoxyfluoroglycopyranosyl residues were also prepared. 1-(6-Deoxy-6-fluoro-/ -D-gluco- and -galacto-pyranosyl)thymine (858 and 860) were obtained from l-/ -D-gluco- and -galacto-pyranosyl-thymine by the usual displacement reaction, or by the condensation method. 

Removal of the 2 -sulfonyloxy group of 859 in a basic medium, followed by reaction with metal halides (LiBr and Nal) or hydrogen halides (HCl-1,4-dioxane, HBr-acetone, or0.1% HFin l,4-dioxane-AlF3)gave, byway of the 2,2 -anhydro intermediate 861, the 2 -halo derivatives 862-865. The 2 -deoxy analog 866 and l-(6-deoxy-6-fluoro- ff-D-mannopyranosyl)thy-mine were also prepared from 864 (R = H) and 861 (R = H), respectively. l-(4-Deoxy-4-fluoro-y -D-glucopyranosyl)thymine was obtained by the condensation method. A different kind of nucleoside, 5-(5-deoxy-5-fluoro-2,3-0-isopropylidene-a-D-ribofuranosyl)-l,3-dimethyluracil has also been prepared. ... 

Addition of a radical to the C6-position of thymine residues in DNA generates the C5-thymine radical 74 (Scheme 8.27). Reaction with molecular oxygen, followed by reduction, yields the hydroperoxide 75. Decomposition of the hydroperoxide ultimately yields the hydantoin nucleobase 78 via the ring-opened derivatives 76 and 77 ti,2 for the decomposition of 75 in aqueous solution is slow, with a 9 h for the tra i-isomer and 20 h for the c -isomer of the nucleoside)... 

Finally a few sentences are deserved for the vast area of DNA photochemistry. Thymine dimerization is the most common photochemical reaction with the quantum yield of formation in isolated DNA of all-thymine oligodeoxynucleotides 2-3% [3], Furthermore, a recent study based on femtosecond time-resolved transient absorption spectroscopy showed that thymine dimers are formed in less than 1 ps when the strand has an appropriate conformation [258], The low quantum yield of the reaction in regular DNA is suggested to be due to the infrequency of these appropriate reactive conformations. 

Durbeej B, Eriksson LA (2002) Reaction mechanism of thymine dimer formation in DNA induced by UV light. Photochem Photobiol A 152 95-101... 

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