Thymine analogs

Dichlorobenzimidazole nucleosides of type 1.2 were prepared (94MI4). The thymine analog, upon selective protection, oxidation, and... 

The thymine analog 5-fluorouracil (5-FU) is converted to 5-fluoro-dUMP, which acts as a suicide inhibitor of thymidylate synthetase. 

Persilylated derivatives of 127 (R = H), when treated with acetoxy ketal 128 followed by addition of potassium iodide and 18-crown-6 in acetonitrile at reflux, gave a 1 1 mixture of N-6-m- 129 and /nz r-nucleosides 130 in 51% yield. Similarly, the thymine analogs were prepared (Equation 12) <1995H(41)87>. 

Like Thr 124 and Thr 215, the Asn 69 and Asn 159 residues occupy equivalent positions in the two homologous motifs of TBP. By analogy with the symmetric binding of a dimeric repressor molecule to a palindromic sequence described in Chapter 8, the two motifs of TBP form symmetric sequence-specific hydrogen bonds to the quasi-palindromic DNA sequence at the center of the TATA box. The consensus TATA-box sequence has an A-T base pair at position 4, but either a T-A or an A-T base pair at the symmetry-related position 5, and the sequence is, therefore, not strictly palindromic. However, the hydrogen bonds in the minor groove can be formed equally well to an A-T base pair or to a T-A base pair, because 02 of thymine and N3 of adenine occupy nearly stereochemically equivalent positions, and it is sufficient, therefore, for the consensus sequence of the TATA box to be quasi-palindromic. 

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]. 

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. ... 

An analogous series of reactions is used to produce depyrimidinated DNA fragments. Hydrazine is used in these reactions, since both cytosine and thymine react with hydrazine. The bases are cleaved to yield urea and a pyrazole ring. The deoxyribose moiety is left as a hydrazone. Piperidine, which reacts with the hydrazone, is used to cleave the nucleotide chain. Cytosines react specifically with hydrazine in 5 mol/ L NaCl, but no specific reaction exists for thymines. Consequently, one aliquot yields labeled oligonu-cleotides 3 -terminated at cytosines, whereas a second aliquot contains nucleotides cleaved in the absence of NaCI at both cytosine and thymine residues. 

Table XIX contains stability constants for complexes of Ca2+ and of several other M2+ ions with a selection of phosphonate and nucleotide ligands (681,687-695). There is considerably more published information, especially on ATP (and, to a lesser extent, ADP and AMP) complexes at various pHs, ionic strengths, and temperatures (229,696,697), and on phosphonates (688) and bisphosphonates (688,698). The metal-ion binding properties of cytidine have been considered in detail in relation to stability constant determinations for its Ca2+ complex and complexes of seven other M2+ cations (232), and for ternary M21 -cytidine-amino acid and -oxalate complexes (699). Stability constant data for Ca2+ complexes of the nucleosides cytidine and uridine, the nucleoside bases adenine, cytosine, uracil, and thymine, and the 5 -monophosphates of adenosine, cytidine, thymidine, and uridine, have been listed along with values for analogous complexes of a wide range of other metal ions (700). Unfortunately comparisons are sometimes precluded by significant differences in experimental conditions.

Platination of the N3 position in 1-substituted uracil and thymine derivatives requires proton abstraction and usually occurs only at high pH, but the Pt-N3 bond, once formed, is thermodynamically stable (log K 9.6) [7]. Platinum binding to N3 increases the basicity of 04, which becomes an additional binding site leading to di- and trinuclear complexes. A list of X-ray structurally characterized species is given by Lippert [7]. Pt complexes of uracil and thymine can form intensely colored adducts (e.g. platinum pyrimidine blues), which show anticar-cinogenic activity analogously to the monomeric species [7]. 

The reaction of silyl ketene acetal addition to nitrones has been used for the synthesis of optically active (2S,3S)-benzoyl- and /V- oc-phenyl isoserine (636a) of isoxazolidine nucleoside-analog of thymine polyoxine C(636b) and of... 

Use of Cl2(PCy3)2RuCHPh for the Synthesis of Thymine-Substituted Polymers as Potential Nucleic Acid Analogs... 

The investigations directed at the synthesis of thymine-substituted polymers demonstrate that the type of functional groups displayed by nucleic acid bases are compatible with ROMP. Moreover, the application of MALDI-TOF mass spectrometry to the analysis of these polymers adds to the battery of tools available for the characterization of ROMP and its products. The utility of this approach for the creation of molecules with the desired biological properties, however, is still undetermined. It is unknown whether these thymine-substituted polymers can hybridize with nucleic acids. Moreover, ROMP does not provide a simple solution to the controlled synthesis of materials that display specific sequences composed of all five common nucleic acid bases. Nevertheless, the demonstration that metathesis reactions can be conducted with such substrates suggests that perhaps neobiopolymers that function as nucleic acid analogs can be synthesized by such processes. 

The deoxy analogs of 2.1 were prepared by coupling l-benzyloxy-2-chloromethoxypropane with silylated thymine, 6-azathymine, uracil, and 6-azauracil to give the anticipated nucleosides 1194 in addition to minor quantities of benzyloxymethylated produce 1195 of type 5.1 (94MI15). None of the deprotected nucleosides exhibited significant activity against HIV. 

Exchange of the existing 5- and 6-protons is faster than the reduction step, so the deuteration of uracil actually produces the tetradeutero derivative 376 <2001JLR7>. Thymine behaves similarly, producing a trideutero derivative <2001JLR7>. Analogous results were seen with the tritiation of uracil, where the tetratritio derivative was obtained <2002MI295>. 

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