Thymine canonical forms

Figure 2 Canonical forms of cytosine, uracil, and thymine...

Spore Photoproduct Lyase. The DNA in spores is in A-form because of dehydration. As a consequence, when spores are exposed to UV, the stereochemistry of the bases is not conducive to the formation of cyclobutane pyrimidine dimers or (6-4) photoproducts. Instead, UV induces the formation of 5-thyminyl-5,6-dihydrothymine or spore photoproduct (SP). This lesion is repaired by a 40-kDa enzyme called SP lyase. The enzyme is an iron-sulfur [4Fe-4S] protein that employs S-adenosyl-methionine (AdoMet) as a catalytic cofactor and carries out repair by a radical mechanism (6) (Fig. 2). In this mechanism, the reduced [Fe-S] center cleaves AdoMet to generate a 5 -deoxyadenosyl radical intermediate and methionine. The radical then abstracts an H-atom from C-6 of the SP. The resulting substrate radical undergoes bond cleavage to generate a product radical. The latter abstracts an H-atom from the 5 deoxyadenosine to form canonical thymines and a 5 deoxyadenosyl radical. Finally, the catalytic cycle is closed by electron transfer back to the [Fe-S] cluster concomitant with the formation of AdoMet (6). 

Nucleobases, such as cytosine, thymine, and uracil are the most important pyrimidine derivatives. In a recent gas-phase study [64], three low-energy tautomers were identified on the basis of CCSD(T)/cc-pVQZ energy calculations andMP2/6-311++G(2d,2p) estimation ofthe vibrational frequencies. The authors emphasize the importance of the high-level estimation of the frequencies and the related thermal correction in order to obtain rehable AG within a 0.7 kcal mol free energy range of the tautomers at T = 450 K. The lowest-free-energy structure is the canonical hydroxy-amine form of cytosine. 

Besides the canonical triplexes formed, for example, between thymine and the adenine-thymine base pair and cytosine and the guanine-cytosine base pair other combinations have been suggested to form stable triplexes, e.g. G-TA, G-GC and T-GC [43], The stability of triplexes depends on pH, ionic strength, temperature, and, in cases where the Watson-Crick duplex is part of a plasmid DNA, it depends on supercoil density [44]. 

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