Thymine, configuration

Of the six possible uracil-uracil (thymine-thymine) configurations, five have been observed experimentally. 

There are four possible structures for such a product (LXXVa-d). The thymine ice-dimer was proven to have the cis-syn configuration (LXXVa) by transformation into an isomer shown to be a derivative of 3,5,9-triazatri-cyclo[5,3,0,0 ] decane of cis-cis-cis configuration (LXXVI) [535-536]. 

Various isomers of 2,3-difluoro-2,3-dideoxynucleosides have been synthesized (Figure 6.7). The configuration of the fluorine atoms plays an essential role in the antiviral activity. ° In the case of the D-lyxo compound, coupling with thymine has failed, due to the participation of the protecting group. 

The close correspondence of the DNA absorption spectrum with that of a mixture of mononucleotides of the same composition illustrates the weak nature of the interactions between neighboring purine and pyrimidine bases guanine (G), cytosine (C), adenine (A), and thymine (T) at an interplanar separation of 3.36 A in the unexcited double-helical configuration. On the other hand the structureless fluorescence band of (calf-thymus) DNA is red-shifted by 3500 cm-1 from the fluorescence spectral origin of the mononucleotides it closely resembles the fluorescence spectrum of the dinocleotide ApT (and of poly dAT) and is accordingly identified131 with the fluorescence... 

Perhaps the best-characterized lesion in DNA associated with uv inactivation and mutagenesis is that involving the intrastrand photodimerization of adjacent thymine residues this lesion is almost wholly repaired by photodissociation of the dimers at shorter wavelengths in the photoreactivation process. Production of the chh dimer in this case, promoted by the configuration of adjacent molecules on the same sugar-phosphate strand, must however involve a rotational displacement of 36°, following the reduction of 0.6 A in molecular separation. 

The second difference concerns the conformation about the thymine-deoxyribose bond of dTTP, which in the ternary complex has the configuration corresponding to a nucleotidyl unit in the product, i.e. double helical DNA. This may represent an error-preventing mechanism 338 The RNA polymerases are more complex.339 They contain two Zn2+ per molecule, although additional zinc may bind at the Mg2+ site with inhibition. There may well be multiple roles for Zn2+, both structural and catalytic. The two sites in the enzyme from B. subtilis have different340 affinities for Zn2+, in accord with this proposition. The enzyme from E. coli has at least five subunits. Zn2+ is located on the subunit which binds DNA and on the subunit on which the initiation and elongation nucleotide binding sites are located.341... 

In Section III.B.2, the difficulties inherent in the use of insoluble unmodified heterocycles were described, together with some methods of overcoming this difficulty reported by Benneche and Undheim. This problem is also encountered in the field of uracils. Thus, the same authors reported the Pd(0)-catalyzed allylation of the bis-(O-trimethylsilyl) derivative of thymine (181) which gives directly the mono- and the bis-JV-allylated products 182 and 183 (Scheme 41). The same reaction with rac-160 affords rac-184, with overall retention of configuration (92ACS761). 

The employed computational methodology allowed us to explain the PES spectra of AT- and MAMT- in the gas phase. Simultaneously, we demonstrated that PT induced by electron attachment, important for the unconstrained AT complexes, is irrelevant for the biologically essential Watson-Crick configuration as modeled by the MAMT complex. Nevertheless, the Watson-Crick MAMT structure binds an excess electron that localizes on thymine, by 7.7 kcal/mol (see structure aMA% °MT in Table 21-1 and Figure 21-23). 

Uracil (or thymine) has hydrogen-bonding functions on four adjacent positions with two donors (D) N(1)H, N(3)H and two acceptors (A) 0(2), 0(4). Hydrogen-bonded dimers can be formed in six possible configurations involving two bonds each denoted UUM2. 

The centrosymmetrical UU12 configuration (Fig. 16.2) occurs frequently as in thymine [THYMIN] thymine monohydrate [THYMMH] Dihydrouracil [DHU-RAC10] dihydrothymidine [DHTHYD10] 6-methyluracil-5-acetic acid [MUR-CAC] 5,6-dihydro-2-thiouracil [DHTURC] 6-methyl-5,6-dihydrouracil [MDH-URC10] 2,4-dithiouracil [DTURAC]. 

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