Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.     

Oxygenase‐Catalyzed Desymmetrization of N,N‐Dialkyl‐piperidine‐4‐carboxylic Acids

γ‐Butyrobetaine hydroxylase (BBOX) is a 2‐oxoglutarate dependent oxygenase that catalyzes the final hydroxylation step in the biosynthesis of carnitine. BBOX was shown to catalyze the oxidative desymmetrization of achiral N,N‐dialkyl piperidine‐4‐carboxylates to give products with two or three stereogenic centers.     

σ‐Hole Bond Versus Hydrogen Bond: From Tetravalent to Pentavalent N,P, and As Atoms

Ab initio calculations were performed on complexes of ZH₄⁺ (Z=N, P, As) and their fluoro derivatives, ZFH₃⁺ and ZF₄⁺, with a HCN (or LiCN) molecule acting as the Lewis base through the nitrogen electronegative center. It was found that the complexes are linked by the Z? H???N hydrogen bond or another type of noncovalent interaction in which the tetravalent heavy atom of the cation acts as the Lewis acid center, that is, when the Z???N link exists, which may be classified as the σ‐hole bond. The formation of the latter interaction is usually preferable to the formation of the corresponding hydrogen bond. The Z???N interaction may be also considered as the preliminary stage of the S_N2 reaction. This is supported by the observation that for a short Z???N contact, the corresponding complex geometry coincides with the trigonal‐bipyramidal geometry typical for the transition state of the S_N2 reaction. The Z???N interaction for some of complexes analyzed here possesses characteristics typical for covalent bonds. Numerous interrelations between geometrical, topological and energetic parameters are discussed. The natural bond orbital method as well as the Quantum Theory of “Atoms in Molecules” is applied to characterize interactions in the analyzed complexes. The experimental evidences of the existence of these interactions, based on the Cambridge Structure Database search, are also presented. In addition, it is justified that mechanisms of the formation of the Z???N interactions are similar to the processes occurring for the other noncovalent links. The formation of Z???N interaction as well as of other interactions may be explained with the use of the σ‐hole concept.     

Solvent Effect and Reactivity Trend in the Aerobic Oxidation of 1,3‐Propanediols over Gold Supported on Titania: NMR Diffusion and Relaxation Studies

In recent work, it was reported that changes in solvent composition, precisely the addition of water, significantly inhibits the catalytic activity of Au/TiO₂ catalyst in the aerobic oxidation of 1,4‐butanediol in methanol due to changes in diffusion and adsorption properties of the reactant. In order to understand whether the inhibition mechanism of water on diol oxidation in methanol is generally valid, the solvent effect on the aerobic catalytic oxidation of 1,3‐propanediol and its two methyl‐substituted homologues, 2‐methyl‐1,3‐propanediol and 2,2‐dimethyl‐1,3‐propanediol, over a Au/TiO₂ catalyst has been studied here using conventional catalytic reaction monitoring in combination with pulsed‐field gradient nuclear magnetic resonance (PFG‐NMR) diffusion and NMR relaxation time measurements. Diol conversion is significantly lower when water is present in the initial diol/methanol mixture. A reactivity trend within the group of diols was also observed. Combined NMR diffusion and relaxation time measurements suggest that molecular diffusion and, in particular, the relative strength of diol adsorption, are important factors in determining the conversion. These results highlight NMR diffusion and relaxation techniques as novel, non‐invasive characterisation tools for catalytic materials, which complement conventional reaction data.     

First Synthesis of the Inherently Chiral Trans-4′ Bisadduct of C59N Azafullerene by Using Cyclo-[2]-dodecylmalonate as a Tether

The multiaddition chemistry of azafullerene C₅₉N has been scarcely explored, and the isolation of pure bisadducts is in its infancy. Encouraged by the recent regioselective synthesis of the inherently chiral equatorial_face bisadduct of C₅₉N, we focused on the isolation of the first trans-4 bisadduct in a simple two-step approach. The first regioselective synthesis of the trans-4 bisadduct of C₅₉N by using cyclo-[2]-dodecylmalonate as a tether is now reported. The newly synthesized bisadduct has C₁ symmetry, as evidenced by ¹³C NMR, while X-ray crystallography validated the trans-4′ addition pattern. Furthermore, the inherently chiral trans-4′ C₅₉N bisadduct was enantiomerically resolved, and the mirror-image relation of the two enantiomers was probed by circular dichroism spectroscopy. Finally, UV-Vis and redox assays suggested that the addition pattern has a reflection in the light-harvesting and redox properties of the bisadduct.