Structure and function of preQ1 riboswitches

PreQ1 riboswitches help regulate the biosynthesis and transport of PreQ1 (7-aminomethyl-7- deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of PreQ1 riboswitches have been identified (PreQ1-I and PreQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon PreQ1 binding, each of which has distinct unusual features and modes of PreQ1 recognition. These features include an unusually long loop 2 in PreQ1-I pseudoknots and an embedded hairpin in loop 3 in PreQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, and dynamics, and applications to biotechnology of PreQ1 riboswitches

Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human

Telomerase synthesizes the telomeric DNA at the 3′ ends of chromosomes and maintains genome integrity. Telomerase RNA (TR) provides the template for telomere-repeat synthesis within a template/pseudoknot (t/PK) domain that is essential for activity. We investigated the structure and dynamics of the t/PK from medaka fish, which contain the smallest vertebrate TR, using NMR and modeling. Despite differences in length, sequence, and predicted secondary structure with human TR, the remarkable similarities between subdomains, including one newly identified in medaka, reveal a conserved architecture for vertebrate t/PK. Combining our model of the full-length pseudoknot and information from the 9-Å structure of Tetrahymena telomerase, we propose models for the interaction of medaka and human t/PK with telomerase reverse transcriptase, providing insight into function

Dual Synergistic Modulation of Photo-Induced Electron Transfer Processes Between Molecules and Gold Nanopillars for Ultrasensitive Plasmon-Enhanced Raman Scattering.

https://v2.sherpa.ac.uk/id/publication/25610 (Accepted version, pathway A)This work presents a synergistic approach to boost plasmon- or surface-enhanced Raman scattering (SERS) by combining molecular and electrical modulators that fine-tune the electronic structure of metal−molecule interfaces, especially the charge transfer (CT) states, allowing molecular resonances. Paraquat (PQ2+) was interfaced with nanopillar SERS substrates whose surface excess of charge was modulated by intercalating anionic Au complexes (AuCl4−, Au(CN)2−) as well as by applying external electric potentials. Such concurrent dual modulation tuned the energy of the CT states of the substrate−anion−PQ2+ triads in resonance with the excitation laser, resulting in a large enhancement of the PQ2+ SERS bands. The results point to a novel coherent through-bond CT contribution of SERS, analogous to the superexchange mechanism for electron transfer in donor−bridge−acceptor systems. The large amplification enables high sensitivity for detecting PQ2+ and ultimately enables the on-site detection of PQ2+ in unprocessed real samples (coffee drink). This study account for new physicochemical variables affecting electron transfer processes in nanostructured metal-molecule interfaces and provides a path for further exploring chemical strategies for greater Raman enhancement and for developing ultrasensitive Raman platforms.Fundamental Research Program (PNK 7440) of the Korea Institute of Materials Science (KIMS) National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (NRF- 2021R1C1C1010213) Junta de Andalucía/FEDER (UMA18-FEDERJA-049 and P18-RT-4592) Fundacion Ramon Areces (Madrid

Comparison of Repellency Effect of Mosquito Repellents for DEET, Citronella, and Fennel Oil

To confirm that Korean Food and Drug Administration (KFDA) guidelines are applicable to test the efficacy of mosquito repellents, these guidelines were used to test the efficacy and complete protection times (CPTs) of three representative mosquito repellents: N,N-diethyl-3-methylbenzamide (DEET), citronella, and fennel oil. The repellency of citronella oil decreased over time, from 97.9% at 0 h to 71.4% at 1 h and 57.7% at 2 h, as did the repellency of fennel oil, from 88.6% at 0 h to 61.2% at 1 h and 47.4% at 2 h. In contrast, the repellency of DEET remained over 90% for 6 h. The CPT of DEET (360 min) was much longer than the CPTs of citronella (10.5 min) and fennel oil (8.4 min). These results did not differ significantly from previous findings, and hence confirm that the KFDA guidelines are applicable for testing the efficacy of mosquito repellents

Reactivity studies of antitumor active dirhodium compounds with DNA oligonucleotides

The study of the mechanism of action of an antitumor active drug is essential for improving the efficacy and reducing the side effects of the drug as well as for developing better alternatives. In this vein, reactions of dirhodium compounds with DNA oligonucleotides were investigated by the techniques of mass spectrometry, HPLC, and NMR spectroscopic analytical methods. The relative reactivities of three dirhodium compounds, namely Rh2(O2CCH3)4, Rh2(O2CCF3)4, and [Rh2(O2CCH3)2(CH3CN)6](BF4)2, with DNA oligonucleotides were studied and compared to the clinically used anticancer drugs cisplatin and carboplatin using both MALDI and ESI mass spectrometric methods. The compound Rh2(O2CCF3)4 exhibits the highest reactivity among the dirhodium compounds, which is comparable to cisplatin, followed by [Rh2(O2CCH3)2(CH3CN)6](BF4)2, and finally Rh2(O2CCH3)4 which is the least reactive. Various dirhodium-oligonucleotide adducts were detected with both MALDI and ESI methods, which involve substitution of different numbers of the original ligands of the given dirhodium compound. ESI MS was found to be a sufficiently soft ionization method for detecting intact metal adducts, and CID MS-MS was useful for detecting weakly bound species such as axial adducts [M+Rh2(O2CCH3)4] and for comparing the relative bond strength between ligands in the metal adduct. A combination of anion exchange HPLC purification and enzymatic digestion studies of the adducts of Rh2(O2CCH3)4 with the 5'-CCTTCAACTCTC oligonucleotide revealed that Rh2(O2CCH3)4 binds to the center or to the ends of the oligonucleotide sequence by displacement of one or two acetate groups. Kinetic products of the type [M+Rh2(O2CCH3)3] obtained from the reaction of Rh2(O2CCH3)4 with 5'-CTCTCAACTTCC were separated by employing both reverse phase and anion exchange HPLC methods. The adduct that involves binding of the dirhodium unit to the exocyclic N4 atom of C5 and the N7 of A6 was found to be most stable whereas other adducts involving binding of C3 or C12 residues are clearly less stable. Reaction of cis-[Rh2(DAP)(O2CCH3)3(CH3OH)](O2CCH3) (DAP = 1,12- diazaperylene) with 5'-CTCTCAACTTCC produced a major adduct in which DAP group intercalates between 6A and 7A in the double stranded adduct with the rhodium atom that is not coordinated to the DAP group forming a covalent bond to the N7 atom of 6A which lends stability to the adduct

Towards caring classroom: Analysis of teacher-students dialogue in grade 6 in South Korea

This correlation study contributes to seek an alternative approach towards caring classroom by way of integration into daily practice. The possibilities of a teacher and students interaction, which occupies most classroom activities, in facilitating classroom climate around caring were examined through correlation and multiple regression analyses. This strategy is grounded in a review of current deficit-based, decontextualized programs and interventions. In particular, this study investigated the impact of a teacher’s evaluative or non-evaluative feedback on students’ perception of caring classroom, in which studies have overlooked. For that, Wells’ framework for analyzing a teacher-students interaction (Wells, 1999) was used with dichotomous categories, the IRE (initiation/response/evaluation) and the IRF (initiation/response/non-evaluative follow up). This study was conducted in one six grade classroom in South Korea, with one teacher and 28 students being participated. A teacher-students interactions were recorded through ten lessons, and students’ perceptions about their classroom climates were collected by the personal measure called ‘What is Happening In this Class? (WIHIC; Fraser, McRobbie & Fisher, 1996). The WIHIC included four aspects of caring classroom climate: Student cohesiveness, teacher support, cooperation and equity. Both data were then analyzed in order to respond the research questions below: 1. To what extent do IRE and IRF take up classroom dialogue? 2. Does IRE/F proportion of the observed dialogue correlate with student’s caring rating scale? 3. How much impact of the IRE/F pattern dialogue on students’ perception of caring classroom? The results showed that a teacher-students interaction during class has potentials in cultivating caring classroom climate. Especially, the teacher’s dialogic stance on whole classroom interaction was more related to students’ sense of teacher support and equity than the monologic interaction. Significant associations were yielded between the IRE/F and teacher support and between the IRF and equity in the classroom. However, the IRE/F were not significant predictors of student cohesiveness and cooperation in the study; thus, further study is required given the theoretical relevance and the complexity of those dimensions. In addition, the regression models in the study presented the opposite effects of the IRE/F pattern dialogue on a range of aspects of caring classroom, negative and positive respectively. The excerpts from the transcripts were used to support the statistical outcomes of the study

Structure and function of preQ1 riboswitches

PreQ1 riboswitches help regulate the biosynthesis and transport of PreQ1 (7-aminomethyl-7- deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of PreQ1 riboswitches have been identified (PreQ1-I and PreQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon PreQ1 binding, each of which has distinct unusual features and modes of PreQ1 recognition. These features include an unusually long loop 2 in PreQ1-I pseudoknots and an embedded hairpin in loop 3 in PreQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, and dynamics, and applications to biotechnology of PreQ1 riboswitches