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Glycosidic bonds of the form discussed above are known as O-glycosidic bonds, in reference to the glycosidic oxygen that links the glycoside to the aglycone or reducing end sugar. In analogy, one also considers S-glycosidic bonds (which form thioglycosides ), where the oxygen of the glycosidic bond is replaced with a sulfur atom.
A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (ribose or 2'-deoxyribose) whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a ...
For a given glycosidic bond orientation, say Cis, the four naturally occurring bases each have three possible edges for formation of base pairs giving rise to 12 such possible base pairing edge identities, each of which can in principle form base pairing with any edge of another base, irrespective of complementarity.
Cytosine, thymine, and uracil are pyrimidines, hence the glycosidic bonds form between their 1 nitrogen and the 1' -OH of the deoxyribose. For both the purine and pyrimidine bases, the phosphate group forms a bond with the deoxyribose sugar through an ester bond between one of its negatively charged oxygen groups and the 5' -OH of the sugar. [2]
Because most heterocyclic bases contain multiple nucleophilic sites, site selectivity is an important issue in nucleoside synthesis. Purine bases, for instance, react kinetically at N 3 and thermodynamically at N 1 (see Eq. (4)). [4] Glycosylation of thymine with protected 1-acetoxy ribose produced 60% of the N 1 nucleoside and 23% of the N 3 ...
Chemical structures for Watson–Crick and Hoogsteen A•T and G•C+ base pairs. The Hoogsteen geometry can be achieved by purine rotation around the glycosidic bond (χ) and base-flipping (θ), affecting simultaneously C8 and C1 ′ (yellow). [1] A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair.
Most glycosyltransferase enzymes form one of two folds: GT-A or GT-B. Glycosyltransferases (GTFs, Gtfs) are enzymes that establish natural glycosidic linkages.They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur ...
Glycosynthase are derived from glycosidase enzymes, which catalyze the hydrolysis of glycosidic bonds. [2] They were traditionally formed from retaining glycosidase by mutating the active site nucleophilic amino acid (usually an aspartate or glutamate ) to a small non-nucleophilic amino acid (usually alanine or glycine ).