Human DNA polymerase iota is a lesion bypass polymerase of the Y family, capable of incorporating nucleotides opposite a variety of lesions in both near error-free and error-prone bypass. With undamaged templating purines polymerase iota normally favors Hoogsteen base pairing. Polymerase iota can incorporate nucleotides opposite a benzo[a]pyrene-derived adenine lesion (dA*); while mainly error-...

The chemical analysis of caramel, formed upon heating of carbohydrates, remains a significant challenge due to the complexity of the resulting product mixture. Identification of the products formed upon heating of monosaccharides including fructose, mannose, galactose, arabinose and ribose is essential to understand the composition and properties of carbohydrate-rich processed foods. In this wo...

A new series of monosaccharide-based glycolipids devoid of phosphate groups and with two lipid chains were rationally designed by varying the lipid chain lengths and saccharide structure of a α-GalCer-derived lead compound (CCL-34) that is a potent TLR4 agonist. The NF-κB activity of a 60-membered galactosyl serine-based synthetic library containing compounds with various lipid chain lengths wa...

Glycoside hydrolases, the enzymes responsible for hydrolysis of the glycosidic bond in di-, oligo- and polysaccharides, and glycoconjugates, are ubiquitous in Nature and fundamental to existence. The extreme stability of the glycosidic bond has meant these enzymes have evolved into highly proficient catalysts, with an estimated 10(17) fold rate enhancement over the uncatalysed reaction. Such ra...

Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crys...

Deamination of 5-methylcytosine residues in DNA gives rise to the G/T mismatched base pair. In humans this lesion is repaired by a mismatch-specific thymine DNA glycosylase (TDG or G/T glycosylase), which catalyzes specific excision of the thymine base through N-glycosidic bond hydrolysis. Unlike other DNA glycosylases, TDG recognizes an aberrant pairing of two normal bases rather than a damage...

The determination of the energetics of the temperature-dependent two-state N $ S pseudorotational equilibrium through 3JHH analysis in 36 nucleos(t)ides and 3 abasic sugars has allowed us for the first time to quantify the strength of various nucleobase-dependent anomeric and gauche effects, and how their interplay finally steers the sugar conformation. The plots of the pDdependent thermodynami...

The key steps in oligosaccharide synthesis are protectinggroup manipulation and stereoselective glycosylation. Various strategies have emerged to expedite glycosylation, and some of these strategies have been elaborated for automated solid-phase synthesis and one-pot cascade glycosylation. Most glycosylation strategies rely on traditional methods for stereochemical control over glycosidic-bond ...

Chitinase A (ChiA) from the bacterium Serratia marcescens is a hydrolytic enzyme, which cleaves beta-1,4-glycosidic bonds of the natural biopolymer chitin to generate di-N-acetyl-chitobiose. The refined structure of ChiA at 1.55 A shows that residue Asp313, which is located near the catalytic proton donor residue Glu315, is found in two alternative conformations of equal occupancy. In addition,...