Three- thymine

An example of a disease that results from a deletion mutation is cystic fibrosis. The presence of mutated genes in which three thymine bases are absent produces cells in the lungs that are defective in the transport of molecules such as sodium. A result is the accumulation of mucus in the lungs. Bacteria readily colonize the mucus and become resistant to treatments intended to kill them. As... 

Fig. 4.4 The dephosphorylated G(T) vG B-DNA oligomer employed in the hole transfer coupling calculations. As the figure depicts, the hole tunnels from the bottom guanine (in balls and sticks) to the top guanine. The tunneling wall is provided by a series of three thymines (red branch, labeled as bridge ). The counterstrand, C(A) vC, acts as a solvating environment (in yellow, labeled as spectators ) and no hole is allowed to localize on it. Taken from Ref. [67]...

The DNA base pairs guanine (G), cytosine (C), adenine (A) and thymine (T). The uracil-2,6-diaminopyridine pair can also form three hydrogen bonds but has a much lower association constant than G-C. 

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. 

Uracil, thymine, and cytosine have been studied using this technique (89JA2308 and references therein). For uracil and thymine, the dioxo tautomer predominates in the case of cytosine (70), three tautomers were detected, 70a, 70b, and 70c, the last one being the least abundant. The gas-phase tautomeric equilibrium of 2-pyridone 15a and 2-hydroxypyridine 15b has been studied by MW spectroscopy (93JPC46) using both a conventional spectrometer and a jet-cooled millimeter-wave spectrometer. The relative abundances are 3 1 in favor of the hydroxy form 15b, which exists in the Z conformation shown (Scheme 23). 

Pyrimidine and imidazole rings are particularly important in biological chemistry. Pyrimidine, for instance, is the parent ring system in cytosine, thymine, and uracil, three of the five heterocyclic amine bases found in nucleic acids An aromatic imidazole ring is present in histidine, one of the twenty amino acids found in proteins. 

As noted previously, RNA is structurally similar to DNA but contains ribose rather than deoxyribose and uracil rather than thymine. There are three major kinds of RNA, each of which serves a specific function. All three are much smaller molecules than DNA, and all remain single-stranded rather than double-stranded. 

The ability of DNA to replicate lies in its double-helical structure. There is a precise correspondence between the bases in the two strands. Adenine in one strand always forms two hydrogen bonds to thymine in the other, and guanine always forms three hydrogen bonds to cytosine so, across the helix, the base pairs are always AT and GC (Fig. 19.29). Any other combination would not be held together as well. During replication of the DNA, the hydrogen bonds, which are... 

Treatment of the allylic sulfoxide 1227 a with diisopropylethylamine (DIPEA) or of 1227 b with N-trimethylsilyldiethylamine 146 and TMSOTf 20 leads in ca. 90% yield to the quaternary amino derivatives 1228 and 1229 and HMDSO 7 [36] (Scheme 8.15). Tetramethylene sulfoxide 1230 reacts with silylated thymine 1231 in the presence of three equivalents of TMSOTf 20 to give the 4 -thio-nucleoside analogue 1232 and HMDSO 7 [37]. Other silylated pyrimidine, pyridine, and purine bases react analogously with cyclic sulfoxides to give 4 -thio-nucleoside analogues [37, 37a, 38]. 

The DNA structure involves two polyanionic phosphodiester strands linked together by hydrogen bonding of base pairs. The strands can be separated by a denaturation process (melting). The melting temperatnre increases with an increase in guanine (G)-cytosine (C) content, since this base pair possess three hydrogen bonds as compared to just two for the adenine (A)-thymine (T) pair. 

The ab initio molecular dynamics study by Hudock et al. discussed above for uracil included thymine as well [126], Similarly to uracil, it was found that the first ultrafast component of the photoelectron spectra corresponds to relaxation on the S2 minimum. Subsequently a barrier exists on the S2 surface leading to the conical intersection between S2 and Si. The barrier involves out-of-plane motion of the methyl group attached to C5 in thymine or out-of-plane motion of H5 in uracil. Because of the difference of masses between these two molecules, kinematic factors will lead to a slower rate (longer lifetime) in thymine compared to uracil. Experimentally there are three components for the lifetimes of these systems, a subpicosecond, a picosecond and a nanosecond component. The picosecond component, which is suggested to correspond to the nonadiabatic S2/S1 transition, is 2.4 ps in uracil and 6.4 ps in thymine. This difference in the lifetimes could be explained by the barrier described above. 

Tables 11-6, 11-7, and 11-8 show calculated solvatochromic shifts for the nucle-obases. Solvation effects on uracil have been studied theoretically in the past using both explicit and implicit models [92, 94, 130, 149, 211-214] (see Table 11-6). Initial studies used clusters of uracil with a few water molecules. Marian et al. [130] calculated excited states of uracil and uracil-water clusters with two, four and six water molecules. Shukla and Lesczynski [122] studied uracil with three water molecules using CIS to calculate excitation energies. Improta et al. [213] used a cluster of four water molecules embedded into a PCM and TDDFT calculations to study the solvatochromic shifts on the absorption and emission of uracil and thymine. Zazza et al. [211] used the perturbed matrix method (PMM) in combination with TDDFT and CCSD to calculate the solvatochromic shifts. The shift for the Si state ranges between (+0.21) - (+0.54) eV and the shift for the S2 is calculated to be between (-0.07) - (-0.19) eV. Thymine shows very similar solvatochromic shifts as seen in Table 11-6 [92],...

M The DNA bases guanine and cytosine can form three hydrogen bonds, whereas adenine and thymine only form two (gray carbon, white hydrogen, red oxygen, blue nitrogen). 

Nucleic acids can contain of any one of three kinds of pyrimidine ring systems (uracil, cytosine, or thymine) or two types of purine derivatives (adenine or guanine). Adenine, guanine, thymine, and cytosine are the four main base constituents found in DNA. In RNA molecules, three of these four bases are present, but with thymine replaced by uracil to make up the fourth. Some additional minor derivatives are found in messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA), particularly the N4,N4-dimethyladenine and N7-methylguanine varieties. 

Figure 1.42 The three pyrimidine bases common to nucleic acid construction. Cytosine and thymine are found in DNA, while in RNA, uracil residues replace thymine. The associated sugar groups are bound in N-glycosidic linkages to the N-l nitrogen.

A nucleoside consists of a purine or pyrimidine base linked to a pentose, either D-ribose to form a ribonucleo-side or 2-deoxy-D-ribose to form a deoxyribonucleoside. Three major purine bases and their corresponding ribo-nucleosides are adenine/adenosine, guanine/guanosine and hypoxanthine/inosine. The three major pyrimidines and their corresponding ribonucleosides are cytosine/ cytodine, uracil/uradine and thymine/thymidine. A nucleotide such as ATP (Fig. 17-1) is a phosphate or polyphosphate ester of a nucleoside. 

The tautomerisation of the purine bases adenine and guanine and of the pyrimidine bases thymine, cytosine, and uracil has important implications in molecular biology, and the occurrence of rare tautomeric forms of these bases has been suggested as a possible cause of spontaneous mutagenesis (Lowdin, 1965 Pullman and Pullman, 1971 Kwiatowski and Pullman, 1975). Three of the most likely tautomers for cytosine are shown in [87]—[89], together with the less likely imino forms [90] and [91] (Scanlan and Hillier,... 

The genetic code is composed of four letters —two pyrimidine nitrogenous bases, thymine and cytosine, and two purine bases, guanine and adenine—which can be regarded functionally as arranged in codons (or triplets). Each codon consists of a combination of three letters therefore, 43 (64) different codons are possible. Sixty-one codons code for specific amino acids (three produce stop signals), and as only 20 different amino acids are used to make proteins, one amino acid can be specified by more than one codon. 

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