High Sensitivity of Human Translesion DNA Synthesis Polymerase κ to Variation in O6-Carboxymethylguanine Structures.

Carboxymethylation of DNA, including the formation of the DNA adduct O6-carboxymethylguanine ( O6-CMG), is associated with lifestyle factors, such as diet. It can impede replicative polymerases (Pols) and lead to replication fork stalling, or an alternative means for replication to proceed by translesion DNA synthesis (TLS). TLS requires specialized DNA Pols characterized by open and preformed active sites capable of preferential bypass of alkylated DNA adducts but that have high error rates, leading to mutations. Human TLS Pols can bypass O6-CMG with varying degrees of accuracy, but it is not known how the chemical structure of the O6-CMG adduct influences polymerase proficiency or fidelity. To better understand how adduct structure determines dNTP selection at lesion sites, we prepared DNA templates with a series of O6-CMG structural analogs and compared the primer extension patterns of Y- and X-family Pols in response to these modifications. The results indicate that the structure of the DNA adduct had a striking effect on dNTP selection by Pol κ and that an increased steric size influences the fidelity of Pol η, whereas Pol ι and ß function were only marginally affected. To test the hypothesis that specific hydrogen bonding interactions between the templating base and the incoming dNTP are a basis of this selection, we modeled the structural analogs with incoming dNTP in the Pol κ active site. These data indicate that the base pairing geometry and stabilization by a dense hydrogen bonding network are important molecular features for dNTP incorporation, providing a basis for understanding error-free bypass of O6-CMG by Pol κ.

Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction.

Cu(i) carbenes derived from α-diazocarbonyl compounds lead to selective alkylation of the O6 position in guanine (O6-G) in mono- and oligonucleotides. Only purine-type lactam oxygens are targeted - other types of amides or lactams are poorly reactive under conditions that give smooth alkylation of guanine. Mechanistic studies point to N7G as a directing group that controls selectivity. Given the importance of O6-G adducts in biology and biotechnology we expect that Cu(i)-catalyzed O6-G alkylation will be a broadly used synthetic tool. While the propensity for transition metals to increase redox damage is well-appreciated, our results suggest that transition metals might also increase the vulnerability of nucleic acids to alkylation damage.

Comparison of boron-assisted oxime and hydrazone formations leads to the discovery of a fluorogenic variant.

We use kinetic data, photophysical properties, and mechanistic analyses to compare recently developed high-rate constant oxime and hydrazone formations. We show that when Schiff base formation between aldehydes and arylhydrazines is carried out with an appropriately positioned boron atom, then aromatic B-N heterocycles form irreversibly. These consist of an extended aromatic structure amenable to the tailoring of specific properties such as reaction rate and fluorescence. The reactions work best in neutral aqueous buffer and can be designed to be fluorogenic - properties which are particularly interesting in bioconjugation.

De novo chemoenzymatic synthesis of sialic acid.

A chemoenzymatic synthesis of sialic acid from inexpensive N-acetyl-D-glucosamine is described. In a three-step Wittig-protection-ozonolysis strategy manno-configured aldehydes are obtained. Treatment with oxaloacetate in the presence of macrophomate synthase affords the signature α-keto-γ-hydroxy acid moiety with high diastereoselectivity.

An artificial metalloenzyme for olefin metathesis.

A Grubbs-Hoveyda type olefin metathesis catalyst, equipped with an electrophilic bromoacetamide group, was used to modify a cysteine-containing variant of a small heat shock protein from Methanocaldococcus jannaschii. The resulting artificial metalloenzyme was found to be active under acidic conditions in a benchmark ring closing metathesis reaction.

Chemoenzymatic synthesis of differentially protected 3-deoxysugars.

3-Deoxysugars are important constituents of complex carbohydrates. For example, 2-keto-3-deoxy-D-manno-octulosonic acid (KDO) is an essential component of lipopolysaccharides in Gram-negative bacteria, 2-keto-3-deoxy-D-glycero-D-galacto-nonulosonic acid (KDN) is widely found in carbohydrates of the bacterial cell wall and in lower vertebrates, and sialic acid is a common cap of mammalian glycoproteins. Although ready access to such sugars would benefit the creation of vaccine candidates, antibiotics and small-molecule drugs, their chemical synthesis is difficult. Here we present a simple chemoenzymatic method for preparing differentially protected 3-deoxysugar derivatives from readily available starting materials. It exploits the promiscuous aldolase activity of the enzyme macrophomate synthase (MPS) to add pyruvate enolate diastereoselectively to a wide range of structurally complex aldehydes. A short synthesis of KDN illustrates the utility of this approach. Enzyme promiscuity, which putatively fosters large functional leaps in natural evolution, has great promise as a source of synthetically useful catalytic transformations.

Efficient enantioselective synthesis of functionalized tetrahydropyrans by Ru-catalyzed asymmetric ring-opening metathesis/cross-metathesis (AROM/CM).

An efficient method for enantioselective synthesis of highly functionalized pyrans (up to 98% ee) through Ru-catalyzed asymmetric ring-opening metathesis/cross-metathesis is described. Reactions are promoted by a recyclable chiral Ru-chloride or a new chiral Ru-iodide complex; the latter catalyst is less efficient but gives rise to significantly higher levels of enantioselectivity. Catalytic reactions can be performed in undistilled solvent and with a wide range of substrates, including those that contain secondary and tertiary alcohols. Representative regioselective functionalizations that highlight the utility of the catalytic method are also presented.

Ru complexes bearing bidentate carbenes: from innocent curiosity to uniquely effective catalysts for olefin metathesis.

The discovery and development of a new class of Ru-based catalysts for olefin metathesis is described. These catalysts, particularly those that do not bear a phosphine ligand, have been demonstrated to promote unique levels of reactivity in a variety of olefin metathesis reactions. The design and development of supported and chiral optically pure variants of this class of Ru catalysts for use in enantioselective metathesis are discussed as well. All catalysts are air stable, reusable, and can be employed with unpurified solvents.

Chiral Ru-based complexes for asymmetric olefin metathesis: enhancement of catalyst activity through steric and electronic modifications.

Design, synthesis, characterization, and catalytic activity of six enantiomerically pure Ru-based metathesis catalysts are disclosed (3a-3f). The new chiral catalysts were prepared through steric and electronic alterations of the parent catalyst system (3). The present studies indicate that the effect of structural modifications of chiral complex 3 does not always correspond to those of the related achiral complexes. The present findings illustrate that modified Ru complexes (3e and 3f) deliver reactivity levels that are more than 2 orders of magnitude higher than 3. Reactivity and physical data are provided that shed light on the origin of activity differences. Some members of the new generation of chiral Ru catalysts promote asymmetric ring-opening (AROM) and ring-closing (ARCM) metatheses that cannot be effected by the first generation chiral catalyst (3).