87 research outputs found

    The role of boronic acids in accelerating condensation reactions of [small alpha]-effect amines with carbonyls

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    A broad palette of bioconjugation reactions are available for chemical biologists, but an area that still requires investigation is high-rate constant reactions. These are indispensable in certain applications, particularly for in vivo labelling. Appropriately positioned boronic acids accelerate normally sluggish Schiff base condensations of α-effect nucleophiles by five orders of magnitude – providing a new entry to the rare set of reactions that have a rate constant above 100 M−1 s−1 under physiological conditions. I summarize here a number of recent reports, including work from my own group, and outline a mechanistic picture that explains the differing behaviour of seemingly similar substrate classes

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

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    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

    The pKa of Bronsted acids controls their reactivity with diazo compounds

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    We study the O-alkylation of phosphate groups by alkyl diazo compounds in a range of small molecules and biopolymers. We show that the relatively high pKa of phosphate in comparison to the other naturally occurring BrĂžnsted acids can be exploited to control alkylation selectivity. We provide a simple protocol for chemical modification of some of the most important instances of phosphates in natural compounds including in small molecule metabolites, nucleic acids, and peptides

    Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction

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    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

    Profiling the Nucleobase and Structure Selectivity of Anticancer Drugs and other DNA Alkylating Agents by RNA Sequencing

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    Drugs that covalently modify DNA are components of most chemotherapy regimens, often serving as first‐line treatments. Classically, the reactivity and selectivity of DNA alkylating agents has been determined in vitro with short oligonucleotides. A statistically sound analysis of sequence preferences of alkylating agents is untenable with serial analysis methods because of the combinatorial explosion of sequence possibilities. Next‐generation sequencing (NGS) is ideally suited for the broad characterization of sequence or structure selectivities because it analyzes many sequences at once. Herein, NGS is used to report on the chemoselectivity of alkylating agents on RNA and this technology is applied to the previously uncharacterized alkylating agent trimethylsilyl diazomethane

    Divergent Synthesis of Bioactive Dithiodiketopiperazine Natural Products Based on a Double C(sp3)−H Activation Strategy

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    This article provides a detailed report of our efforts to synthesize the dithiodiketopiperazine (DTP) natural products (−)‐epicoccin G and (−)‐rostratin A using a double C(sp3)−H activation strategy. The strategy's viability was first established on a model system lacking the C8/C8’ alcohols. Then, an efficient stereoselective route including an organocatalytic epoxidation was secured to access a key bis‐triflate substrate. This bis‐triflate served as the functional handles for the key transformation of the synthesis: a double C(sp3)−H activation. The successful double activation opened access to a common intermediate for both natural products in high overall yield and on a multigram scale. After several unsuccessful attempts, this intermediate was efficiently converted to (−)‐epicoccin G and to the more challenging (−)‐rostratin A via suitable oxidation/reduction and protecting group sequences, and via a final sulfuration that occurred in good yield and high diastereoselectivity. These efforts culminated in the synthesis of (−)‐epicoccin G and (−)‐rostratin A in high overall yields (19.6 % over 14 steps and 12.7 % over 17 steps, respectively), with the latter being obtained on a 500 mg scale. Toxicity assessments of these natural products and several analogues (including the newly synthesized epicoccin K) in the leukemia cell line K562 confirmed the importance of the disulfide bridge for activity and identified dianhydrorostratin A as a 20x more potent analogue

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

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    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 Îș and that an increased steric size influences the fidelity of Pol η, whereas Pol Îč and ÎČ 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 Îș 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 Îș

    Quantum-chemistry-aided identification, synthesis and experimental validation of model systems for conformationally controlled reaction studies: separation of the conformers of 2,3-dibromobuta-1,3-diene in the gas phase

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    The Diels-Alder cycloaddition, in which a diene reacts with a dienophile to form a cyclic compound, counts among the most important tools in organic synthesis. Achieving a precise understanding of its mechanistic details on the quantum level requires new experimental and theoretical methods. Here, we present an experimental approach that separates different diene conformers in a molecular beam as a prerequisite for the investigation of their individual cycloaddition reaction kinetics and dynamics under single-collision conditions in the gas phase. A low- and high-level quantum-chemistry-based screening of more than one hundred dienes identified 2,3-dibromobutadiene (DBB) as an optimal candidate for efficient separation of itsgaucheand s-transconformers by electrostatic deflection. A preparation method for DBB was developed which enabled the generation of dense molecular beams of this compound. The theoretical predictions of the molecular properties of DBB were validated by the successful separation of the conformers in the molecular beam. A marked difference in photofragment ion yields of the two conformers upon femtosecond-laser pulse ionization was observed, pointing at a pronounced conformer-specific fragmentation dynamics of ionized DBB. Our work sets the stage for a rigorous examination of mechanistic models of cycloaddition reactions under controlled conditions in the gas phase

    Nanopore Sequencing Accurately Identifies the Mutagenic DNA Lesion O; 6; -Carboxymethyl Guanine and Reveals Its Behavior in Replication

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    O; 6; -carboxymethylguanine (O; 6; -CMG) is a highly mutagenic alkylation product of DNA, triggering transition mutations relevant to gastrointestinal cancer. However, precise localization of a single O; 6; -CMG with conventional sequencing platforms is challenging. Here nanopore sequencing (NPS), which directly senses single DNA bases according to their physiochemical properties, was employed to detect O; 6; -CMG. A unique O; 6; -CMG signal was observed during NPS and a single-event call accuracy of >95 % was achieved. Moreover, O; 6; -CMG was found to be a replication obstacle for Phi29 DNA polymerase (Phi29 DNAP), suggesting this lesion could cause DNA sequencing biases in next generation sequencing (NGS) approaches
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