Thymine bases

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). 

Figure 10.22 Sequence-specific interactions between one of the a-helical basic regions of GCN4 (blue) and bases in the DNA fragment (red). The methyl groups of the thymine bases are shown as spheres.

Samoylova E, Lippert H, Ullrich S, Hertel IV, Radloff W, Schultz T, (2005) Dynamics of photoinduced processes in adenine and thymine base pairs. J Am Chem Soc 127 1782—1786... 

Sobolewski AL, Domcke W (2006) Role of electron-driven proton-transfer processes in the excited-state deactivation adenine-thymine base pair. J Phys Chem A 110 9031-9038... 

Single stranded oligomers exhibit a completely different behavior than double strands. As shown in Fig. 6, the increase of the number n of thymine bases in the bridge between the electron donor guanine and the enol ether radical cation as electron acceptor influence the rate of the electron transfer only slightly. This can be explained by the flexibility of the single strand, which levels out the distance between donor and acceptor [13]. 

In general, reduction potentials of nucleobases have been studied much less than their oxidation potentials, and in particular water-based data are rather lacking [2, 35]. We therefore listed the available polarographic potentials measured in dimethylformamide and data obtained from pulse radiolysis studies or fluorescence quenching measurements. From the data in Table 1, it is evident that the pyrimidine bases are most easily reduced. The reduction potential of the T=T CPD lesion is close to the estimated value of the undamaged thymine base [34, 36]. 

Psoralens can react by two different routes upon photoactivation (Parsons, 1980 Pathak, 1984). The first route is through the well-known photoreaction mechanism that principally involves intercalation within double-stranded DNA or RNA with the formation of adducts with adjacent thymine bases. The furan-side and pyrone-side rings in psoralen both can form cycloaddition products with the 5,6-double bond of thymine to create a crosslink between two DNA strands (Reaction 57) or to a lesser extent, within double-strand regions of RNA. 

Figure 11.15 The photoreactive compound psoralen-PEC>3-biotin can intercalate into double stranded DNA or RNA segments and covalently link to thymine bases via a photoreaction process.

The molecular weights of the polymers before and after irradiation were followed by GPC to determine changes in the molecular weights of the polyamides. It was found that photolysis of the polymer resulted in polymer chain scission, leading to the appearance of oligomers containing thymine bases at the end of the molecules. 

Table II. Lithographic Evaluation of Polymethacrylates with Pendant Thymine bases...

Table III. Quantum Yields and Maximum Photodimerization Conversion of Thymine Bases in Polymethacrylates with Pendant Thymine Bases in the Film State...

Another pyrimidine base, uracil, is found in RNA instead of thymine. Base pairing between adenine and uracil involves two hydrogen bonds and resembles the adenine-thymine interaction. This type of base pairing is of importance in transcription, the synthesis of messenger RNA (see Section 14.2.5). 

Ultraviolet l fyt causes neighboring thymine bases to form thymine dimers that block replication and gene expression. 

Nowick JS, Chen JS. Molecular recognition in aqueous micellar solution—adenine thymine base-pairing in SDS micelles. J Am Chem Soc 1992 114 1107-1108. 

There is not much discussion of thymine oxidation products since they are viewed as unimportant in the radiation chemistry of DNA, the feeling being that in DNA, most of the holes will be trapped by the purines. However, when model systems are used, there are several known pathways that involve oxidation of the thymine base. When a thymine base is ionized, the resulting thymine cation is an acid with for deprotonation in... 

RNA to initiate cDNA synthesis. All cellular mRNA contains multiple repeats of adenine bases (poly-A tails). Therefore the complementary thymine bases (oligo-dT) can be used as a primer that binds to the mRNA template required for the reverse transcriptase to synthesize the cDNA. In the case of pancreatic mRNAs (Figure 4.2), the signihcantly higher mRNA for insulin compared with other proteins allowed success in isolating the insulin-specihc cDNA. Subsequent insertion of cDNA into a bacterial expression vector allowed the production of functional insulin that is now marketed as a successful therapeutic product (Figure 4.2). 

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