Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics

Sequence-selective chemical modification of DNA by synthetic ligands has been a long-standing challenge in the field of chemistry. Even when the ligand consists of a sequence-specific DNA binding domain and reactive group, sequence-selective reactions by these ligands are often accompanied by off-target reactions. A basic principle to design DNA modifiers that react at specific sites exclusively governed by DNA sequence recognition remains to be established. We have previously reported selective DNA modification by a self-ligating protein tag conjugated with a DNA-binding domain, termed as a modular adaptor, and orthogonal application of modular adaptors by relying on the chemoselectivity of the protein tag. The sequence-specific crosslinking reaction by the modular adaptor is thought to proceed in two steps: the first step involves the formation of a DNA–protein complex, while in the second step, a proximity-driven intermolecular crosslinking occurs. According to this scheme, the specific crosslinking reaction of a modular adaptor would be driven by the DNA recognition process only when the dissociation rate of the DNA complex is much higher than the rate constant for the alkylation reaction. In this study, as a proof of principle, a set of combinations for modular adaptors and their substrates were utilized to evaluate the reactions. Three types of modular adaptors consisting of a single type of self-ligating tag and three types of DNA binding proteins fulfill the kinetic requirements for the reaction of the self-ligating tag with a substrate and the dissociation of the DNA–protein complex. These modular adaptors actually undergo sequence-specific crosslinking reactions exclusively driven by the recognition of a specific DNA sequence. The design principle of sequence-specific modular adaptors based on the kinetic aspects of complex formation and chemical modification is applicable for developing recognition-driven selective modifiers for proteins and other biological macromolecules

Suppression of Fast Proton Conduction by Dilution of a Hydronium Solvate Ionic Liquid: Localization of Ligand Exchange

A dilution effect on the proton conduction of a hydronium solvate ionic liquid [H₃O⁺centerdot18C6]Tf₂N, which consists of hydronium ion (H₃O⁺), 18-crown-6-ether ligand (18C6), and bis[(trifluoromethyl)sulfonyl]amide anion (Tf₂N⁻; Tf = CF₃SO₂), has been studied. When [H₃O⁺･18C6]Tf₂N was diluted using equimolar 18C6 solvent, the distinctive fast proton conduction in [H₃O⁺･18C6]Tf₂N was suppressed in stark contrast to the case of common protic ionic liquids. Nuclear magnetic resonance spectroscopy showed that the fast exchange between free 18C6 molecules and coordinated ones, suggesting that the added solvent had induced a local proton exchange rather than a cooperative proton relay

Proton conduction in hydronium solvate ionic liquids affected by ligand shape

We investigated the ligand dependence of the proton conduction of hydronium solvate ionic liquids (ILs), consisting of a hydronium ion (H₃O⁺), polyether ligands, and a bis[(trifluoromethyl)sulfonyl]amide anion (Tf₂N⁻; Tf = CF₃SO₂). The ligands were changed from previously reported 18-crown-6 (18C6) to other cyclic or acyclic polyethers, namely, dicyclohexano-18-crown-6 (Dh18C6), benzo-18-crown-6 (B18C6) and pentaethylene glycol dimethyl ether (G5). Pulsed-field gradient spin echo nuclear magnetic resonance results revealed that the protons of H₃O⁺ move faster than those of cyclic 18C6-based ligands but as fast as those of acyclic G5 ligands. Based on these results and density functional theory calculations, we propose that the coordination of a cyclic ether ligand to the H₃O⁺ ion is essential for fast proton conduction in hydronium solvate ILs. Our results attract special interest for many electro- and bio-chemical applications such as electrolyte systems for fuel cells and artificial ion channels for biological cells

Glyme-Lithium Bis(trifluoromethylsulfonyl)amide Super-concentrated Electrolytes: Salt Addition to Solvate Ionic Liquids Lowers Ionicity but Liberates Lithium Ions

Solvate ionic liquids (ILs) such as binary equimolar mixtures of glymes (ethyleneglycol-dimethylether or CH₃(OCH₂CH₂)nOCH₃) and lithium bis(trifluoromethylsulfonyl)amide (LiTf₂N; Tf = SO₂CF₃) are known to show identical self-diffusion coefficients for glymes and Li⁺ ions. Here, we report that the addition of LiTf₂N to the solvate ILs drastically changes their electrolyte properties. When the lithium salts are added to give the super-concentrated electrolytes with [O]/[Li⁺] = 3 (molar ratio of ether oxygen to Li⁺), ligand exchange or hopping conduction of Li⁺ takes place for triglyme (G3; n = 3) and tetraglyme (G4; n = 4). In addition, the Li⁺ transference number tLi⁺(EC), electrochemically measured under anion blocking conditions, increases about 3–6 times compared with the solvate ILs. Consequently, segmental motion of glymes apparently affects the transport properties even for the shorter G3 in the super-concentrated region. The relationship between the coordination structure and the transport properties are also discussed as a function of ionicity, the extent of the contribution of self-diffusion to the actual ion conduction. Plots vs ionicity demonstrate that a clear line can be drawn between the solvate ILs and the super-concentrated electrolytes

Anti-prion activity of an RNA aptamer and its structural basis.

Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrP(C)) of PrP into an abnormal form (PrP(Sc)) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrP(C) is expected to block this conversion and to thereby prevent prion diseases. Here, we show that an RNA aptamer comprising only 12 residues, r(GGAGGAGGAGGA) (R12), reduces the PrP(Sc) level in mouse neuronal cells persistently infected with the transmissible spongiform encephalopathy agent. Nuclear magnetic resonance analysis revealed that R12, folded into a unique quadruplex structure, forms a dimer and that each monomer simultaneously binds to two portions of the N-terminal half of PrP(C), resulting in tight binding. Electrostatic and stacking interactions contribute to the affinity of each portion. Our results demonstrate the therapeutic potential of an RNA aptamer as to prion diseases

A Hydronium Solvate Ionic Liquid: Facile Synthesis of Air-Stable Ionic Liquid with Strong Bronsted Acidity

This was Paper 3475 presented at the Honolulu, Hawaii, Meeting of the Society, October 2–7, 2016.A new kind of ionic liquid (IL) with strong Brønsted acidity, i.e., a hydronium (H₃O⁺) solvate ionic liquid, is reported. The IL can be described as [H₃O⁺·18C6]Tf₂N, where water exists as the H₃O⁺ ion solvated by 18-crown-6-ether (18C6), of which the counter anion is bis(trifluoromethylsulfonyl)amide (Tf₂N⁻; Tf = CF₃SO₂). The hydrophobic Tf₂N⁻ anion makes [H₃O⁺·18C6]Tf₂N, evaluated using the indicator method, is a new record for ILs and indicates strong aciditiy. The findings regarding this proton-condensed solvate IL are of fundamental interest, and will help in the design of media for new acid-base reactions

Boost in bioethanol production using recombinant Saccharomyces cerevisiae with mutated strictly NADPH-dependent xylose reductase and NADP(+)-dependent xylitol dehydrogenase.

The xylose-fermenting recombinant Saccharomyces cerevisiae and its improvement have been studied extensively. The redox balance between xylose reductase (XR) and xylitol dehydrogenase (XDH) is thought to be an important factor in effective xylose fermentation. Using protein engineering, we previously successfully reduced xylitol accumulation and improved ethanol production by reversing the dependency of XDH from NAD(+) to NADP(+). We also constructed a set of novel strictly NADPH-dependent XR from Pichia stipitis by site-directed mutagenesis. In the present study, we constructed a set of recombinant S. cerevisiae carrying a novel set of mutated strictly NADPH-dependent XR and NADP(+)-dependent XDH genes with overexpression of endogenous xylulokinase (XK) to study the effects of complete NADPH/NADP(+) recycling on ethanol fermentation and xylitol accumulation. All mutated strains demonstrated reduced xylitol accumulation, ranging 34.4-54.7% compared with the control strain. Moreover, compared with the control strain, the two strains showed 20% and 10% improvement in ethanol production

A novel strictly NADPH-dependent Pichia stipitis xylose reductase constructed by site-directed mutagenesis.

Xylose reductase (XR) and xylitol dehydrogenase (XDH) are the key enzymes for xylose fermentation and have been widely used for construction of a recombinant xylose fermenting yeast. The effective recycling of cofactors between XR and XDH has been thought to be important to achieve effective xylose fermentation. Efforts to alter the coenzyme specificity of XR and HDX by site-directed mutagenesis have been widely made for improvement of efficiency of xylose fermentation. We previously succeeded by protein engineering to improve ethanol production by reversing XDH dependency from NAD(+) to NADP(+). In this study, we applied protein engineering to construct a novel strictly NADPH-dependent XR from Pichia stipitis by site-directed mutagenesis, in order to recycle NADPH between XR and XDH effectively. One double mutant, E223A/S271A showing strict NADPH dependency with 106% activity of wild-type was generated. A second double mutant, E223D/S271A, showed a 1.27-fold increased activity compared to the wild-type XR with NADPH and almost negligible activity with NADH

A two-step screening to optimize the signal response of an auto-fluorescent protein-based biosensor

Auto-fluorescent protein (AFP)-based biosensors transduce the structural change in their embedded recognition modules induced by recognition/reaction events to fluorescence signal changes of AFP. The lack of detailed structural information on the recognition module often makes it difficult to optimize AFP-based biosensors. To enhance the signal response derived from detecting the putative structural change in the nitric oxide (NO)-sensing segment of transient receptor potential canonical 5 (TRPC5) fused to enhanced green fluorescent protein (EGFP), EGFP-TRPC5, a facile two-step screening strategy, in silico first and in vitro second, was applied to variants of EGFP-TRPC5 deletion-mutated within the recognition module. In in silico screening, the structural changes of the recognition modules were evaluated as root-mean-square-deviation (RMSD) values, and 10 candidates were efficiently selected from 47 derivatives. Through in vitro screening, four mutants were identified that showed a larger change in signal response than the parent EGFP-TRPC5. One mutant in particular, 551-575, showed four times larger change upon reaction with NO and H₂O₂. Furthermore, mutant 551-575 also showed a signal response upon reaction with H₂O₂ in mammalian HEK293 cells, indicating that the mutant has the potential to be applied as a biosensor for cell measurement. Therefore, this two-step screening method effectively allows the selection of AFP-based biosensors with sufficiently enhanced signal responses for application in mammalian cells

Partially naked fluoride in solvate ionic liquids

Truly naked fluoride exists only in the gas phase. Fluoride can be stabilized by a complexing agent and an organic cation, resulting in anhydrous or dehydrated fluoride which is “partially naked.” This partially naked fluoride enables fluorination reactions at much lower temperatures than hydrated fluorides. Here we show a simple method for preparing fluoride-based solvate ionic liquids (SILs) by mixing 1-alkyl-3-methylimidazolium (1-ethyl-3-methylimidazolium or 1-butyl-3-methylimidazolium) bromide, silver fluoride (AgF), and EG (1:1:1 in molar ratio) in dry methanol. Removal of the methanol produced anhydrous SILs, [C₂C₁im]F·EG and [C₄C₁im]F·EG. This is the first SIL reported that comprises fluoride. ¹H NMR and infrared spectroscopy reveal fluoride hydrogen bonds with EG OH groups and cation aromatic H atoms but not cation tail group protons. Fluorination reactions on benzyl bromide show that [C₂C₁im]F·EG has high reactivity with reasonable yield under mild conditions, confirming the fluoride ion is partially naked