Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy.

Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is powerful in structure and dynamics study of biological macromolecules by providing distance distribution information ranging from 1.8 to 6 nm, providing that the biomolecules are site-specifically labeled with paramagnetic tags. However, long distances up to 16 nm have been measured on perdeuterated and spin-labeled proteins in deuterated solvent by PELDOR. Here we demonstrate long-range distance measurement on a large RNA, the 97-nucleotide 3'SL RNA element of the Dengue virus 2 genome, by combining a posttranscriptional site-directed spin labeling method using an unnatural basepair system with RNA perdeuteration by enzymatic synthesis using deuterated nucleotides. The perdeuteration removes the coupling of the electron spins of the nitroxide spin labels from the proton nuclear spin system of the RNA and does extend the observation time windows of PELDOR up to 50 µs. This enables one to determine long distances up to 14 nm for large RNAs and their conformational flexibility.

Tailoring the Luminescent Properties of SrS:Ce3+ by Sr-Deficiency and Na+ Doping.

Ce3+-doped SrS phosphors with a charge-compensating Na+ addition were successfully synthesized via a solid-state reaction method, and the related X-ray diffraction patterns can be indexed to the rock-salt-like crystal structure of the Fm3̅m space group. SrS:(Ce3+)x (0.005 ≤ x ≤ 0.05) and SrS:(Ce3+)0.01,(Na+)y (0.005 ≤ y ≤ 0.030) phosphors were excited by 430 nm UV-Vis light, targeted to the 5d1 → 4f1 transition of Ce3+. The composition-optimized SrS:(Ce3+)0.01, (Na+)0.015 phosphors showed an intense broad emission band at λ = 430-700 nm. The doping of Na+ was probed by solid-state nuclear magnetic resonance. The 430 nm pumped white light-emitting diode structure fabricated with a combination of SrS:(Ce3+)0.01,(Na+)0.015 and Sr2Si5N8:Eu2+ phosphors shows a color-rendering index (Ra) of 89.7. The proposed strategy provides new avenues for the design and realization of novel high color quality solid-state LEDs.

[Metabolic fingerprint analysis of RAW264.7 inflammatory cell model by using UPLC-Q-TOF/MS].

In order to reveal the properties of polar metabolome in inflammatory cells, we selected LPS-induced RAW264.7 inflammatory cell models as the carrier for the research of metabolic fingerprint analysis. In this study, an ultra performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF/MS)-based metabolomics protocol was optimized for the extraction of polar metabolites from RAW264.7 cell line. Then orthogonal partial least squares discriminant analysis (OPLS-DA) was used to process the metabolic data, and finally, a total of 17 metabolites were selected and identified. The results showed that MeOH-CHCl3-H2O (8∶1∶1) was chosen as the optimal extraction solvent to achieve higher number of chromatographic peaks, with the best relative extraction efficiency and stability. Comparing with the normal cells, the inflammatory cells presented an abnormal metabolism in protein, carbohydrate, nucleotide and phospholipids. In this study, a UPLC-Q-TOF/MS-based metabolomics protocol for the polar metabolites from RAW264.7 cell line was developed, which may provide important information for the study of mechanism of inflammation and the anti-inflammatory drugs.

[A new method on investigate chemical constituents which have anti-thrombin effect by HPLC].

An in vitro anti-thrombin bioassay was developed to investigate the chemical constituents which have anti-thrombin effect from the water soluble components of Salvia miltiorrhiza. Using Chromozym TH as a probe combined with ethyl acetate Semi-micro extraction was applied to measure p-nitroaniline by HPLC. According to the results, the inactivationrate of thrombin by sodium danshensu, salvianolic acid A and salvianolic acid B under a given set of conditions were 3.06%, 77.77% and 2.35%, respectively. In the water-soluble components, salvianolic acid A has a direct inhibition of thrombin, while sodium danshensu and salvianolic acid B have no significant effect on thrombin. The method is sensitive and low consumption. It can eliminate the interference absorbed for the sample itself which can be used for screening single or multiple direct antithrombin active ingredient of herbal extract.

Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies.

Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Förster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with post-transcriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions. However, due to the bulky sizes of functional groups or labeling probes used, such strategies might cause structural perturbation and decrease the accuracy of distance measurements. Here, we synthesize an α-thiophosphorylated variant of rTPT3TP (rTPT3αS), which allows for post-transcriptional site-specific labeling of large RNAs at the internal α-phosphate backbone via maleimide-modified probes. Subsequent PELDOR, XSI, and smFRET measurements result in narrower distance distributions than labeling at the TPT3 base. The presented strategy provides a new route to empower the molecular rulers for structural and dynamic studies of large RNA and its complex.

pH-dependent rearrangement determines the iron-activation and antitumor activity of artemisinins.

The action mechanisms of artemisinins remains elusive for decades, and one long-standing question is whether the indispensable peroxide group is activated by iron or heme. Although heme usually reacts faster with artemisinins than iron does, we have found that rearrangement of dihydroartemisinin (DHA) into monoketo-aldehyde-peroxyhemiacetal (MKA) under physiological conditions can significantly enhance its reaction towards iron. The rearrangement is pH-dependent and the derived MKA is identified by LC-MS in the cellular metabolites of DHA in cancer cells. MKA reacts quickly with ferrous irons to afford reactive carbon-centered radicals and can inhibit enzyme activities in vitro. Moreover, MKA oxidizes ferrous irons to ferric irons, which may explain the effect of DHA on decreasing cellular labile iron pool (LIP). Both addition of exogenous iron and increase in LIP via triggering ferroptosis can enhance the cytotoxicity of DHA against cancer cells. While artesunate (ATS) can also decompose to MKA after hydrolyzing into DHA, the other artemisinins of lower antitumor activity, e.g. artemisinin (ART), artemether (ATM) and arteether (ATE), exhibit negligible hydrolysis and rearrangement under the same conditions. Our study reveals the vital role of molecular rearrangement to the activation and activity of artemisinins and provides a new strategy for designing antitumor molecules containing endoperoxide group.

Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions.

Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron-Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.

Transition-Metal-Free Borylation of Alkyl Iodides via a Radical Mechanism.

We describe an operationally simple transition-metal-free borylation of alkyl iodides. This method uses commercially available diboron reagents as the boron source and exhibits excellent functional group compatibility. Furthermore, a diverse range of primary and secondary alkyl iodides could be effectively transformed to the corresponding alkylboronates in excellent yield. Mechanistic investigations suggest that this borylation reaction proceeds through a single-electron transfer mechanism featuring the generation of an alkyl radical intermediate.

Mn-Mediated Electrochemical Trifluoromethylation/C(sp2)-H Functionalization Cascade for the Synthesis of Azaheterocycles.

A general electrohemical strategy for the combined trifluoromethylation/C(sp2)-H functionalization using Langlois' reagent as the CF3 source under oxidant-free conditions was developed. Using Mn salts as the redox mediator, this method provides an efficient and sustainable means to access a variety of functionalized heterocycles bearing a CF3 moiety. Detailed mechanistic studies are consistent with the formation of CF3-bound high oxidation state Mn species, suggesting a transition-metal-mediated CF3 transfer mechanism for this trifluoromethylation/C(sp2)-H functionalization process.