Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity

Many RNA structures are composed of simple secondary structure elements linked by a few critical tertiary interactions. SHAPE chemistry has made interrogation of RNA dynamics at single-nucleotide resolution straightforward. However, de novo identification of nucleotides involved in tertiary interactions remains a challenge. Here we show that nucleotides that form noncanonical or tertiary contacts can be detected by comparing information obtained using two SHAPE reagents, N-methylisatoic anhydride (NMIA) and 1-methyl-6-nitroisatoic anhydride (1M6). Nucleotides that react preferentially with NMIA exhibit slow local nucleotide dynamics and usually adopt the less common C2'-endo ribose conformation. Experiments and first-principles calculations show that 1M6 reacts preferentially with nucleotides in which one face of the nucleobase allows an unhindered stacking interaction with the reagent. Differential SHAPE reactivities were used to detect noncanonical and tertiary interactions in four RNAs with diverse structures and to identify preformed noncanonical interactions in partially folded RNAs. Differential SHAPE reactivity analysis will enable experimentally concise, large-scale identification of tertiary structure elements and ligand binding sites in complex RNAs and in diverse biological environments.     

Local influence of boundary conditions on a confined supercooled colloidal liquid

We study confined colloidal suspensions as a model system which approximates the behavior of confined small molecule glass-formers. Dense colloidal suspensions become glassier when confined between parallel glass plates. We use confocal microscopy to study the motion of confined colloidal particles. In particular, we examine the influence particles stuck to the glass plates have on nearby free particles. Confinement appears to be the primary influence slowing free particle motion, and proximity to stuck particles causes a secondary reduction in the mobility of free particles. Overall, particle mobility is fairly constant across the width of the sample chamber, but a strong asymmetry in boundary conditions results in a slight gradient of particle mobility.     

Nanoparticles-chemistry, new synthetic approaches, gas phase clustering and novel applications

In this paper, an overview of the synthesis, chemistry and applications of nanosystems carried out in our laboratory is presented. The discussion is divided into four sections, namely (a) chemistry of nanoparticles, (b) development of new synthetic approaches, (c) gas phase clusters and (d) device structures and applications. In ‘chemistry of nanoparticles’ we describe a novel reaction between nanoparticles of Ag and Au with halocarbons. The reactions lead to the formation of various carbonaceous materials and metal halides. In ‘development of new synthetic approaches’ our one-pot methodologies for the synthesis of core-shell nanosystems of Au, Ag and Cu protected with TiO₂ and ZrO₂ as well as various polymers are discussed. Some results on the interaction of nanoparticles with biomolecules are also detailed in this section. The third section covers the formation of gas phase aggregates/clusters of thiol-protected sub-nanoparticles. Laser desorption of H₂MoO₄, H2WO₄, MoS₂, and WS₂ giving novel clusters is discussed. The fourth section deals with the development of simple devices and technologies using nanomaterials described above.     

Helical cyclic pentapeptides constrain HIV-1 Rev peptide for enhanced RNA binding

HIV-1 Rev is a 116 residue transporter protein that enters the host cell nucleus and uses its 17 amino acid segment (Rev_34–50) to bind and capture a specific piece of RNA, the Rev Response Element (RRE), for transport to the cytoplasm. This is critical for HIV replication. In isolation, Rev_34–50 shows negligible structure in water, but is alpha helical in a mixture of water and 2,2,2-trifluoroethanol (TFE) or when bound to RRE. Here we report that helix-constrained cyclic pentapeptides, either appended to the N-terminus or incorporated within Rev_34–50, are efficient helix nucleators in water. They induce up to 90% alpha helicity for isolated Rev peptides in water and confer high RNA-binding affinity.     

Metal–Organic Frameworks (MOFs) as Safer,Structurally Reinforced Energetics

Second‐generation cobalt and zinc coordination architectures were obtained through efforts to stabilize extremely sensitive and energetic transition‐metal hydrazine perchlorate ionic polymers. Partial ligand substitution by the tridentate hydrazinecarboxylate anion afforded polymeric 2D‐sheet structures never before observed for energetic materials. Carefully balanced reaction conditions allowed the retention of the noncoordinating perchlorate anion in the presence of a strongly chelating hydrazinecarboxylate ligand. High‐quality X‐ray single‐crystal structure determination revealed that the metal coordination preferences lead to different structural motifs and energetic properties, despite the nearly isoformulaic nature of the two compounds. Energetic tests indicate highly decreased sensitivity and DFT calculations suggest a high explosive performance for these remarkable structures.     

Heptyl α‐D‐Mannosides Grafted on a β‐Cyclodextrin Core To Interfere with Escherichia coli Adhesion: An In Vivo Multivalent Effect

n‐Heptyl α‐D ‐mannoside (HM) has previously been identified as a nanomolar FimH antagonist able to prevent Escherichia coli adhesion. We have designed mono‐ and heptavalent glycoconjugates in which HM is tethered to β‐cyclodextrin (β‐CD) through short and long spacers. One‐pot click or co‐clicking procedures were developed to directly obtain the glycoconjugates from unprotected HM and β‐CD precursors. These FimH antagonists were examined biophysically and in vivo. Reverse titrations by isothermal calorimetry led to trapping of the short‐tethered heptavalent β‐CD in a complex with three FimH lectins. Combined dynamic light scattering and small‐angle X‐ray solution scattering data allowed the construction of a model of the FimH trimer. The heptavalent β‐CDs were shown to capture and aggregate living bacteria in solution and are therefore also able to aggregate FimH when attached to different bacteria pili. The first in vivo evaluation of multivalent FimH inhibitors has been performed. The heptavalent β‐CDs proved to be much more effective anti‐adhesive agents than monovalent references with doses of around 2 μg instilled in the mouse bladder leading to a significantly decreased E. coli load. Intravenously injected radiolabeled glycoconjugates can rapidly reach the mouse bladder and >2 μg concentrations can easily be retained over 24 h to prevent fluxing bacteria from rebinding.     

Evaluation of flow restrictors for open-tubular supercritical fluid chromatography at pressures up to 560 atm

Proper performance of the flow restrictor is of crucial importance in supercritical fluid chromatography. This is especially the case when the restrictor is the interface between the chromatographic column and a detector operating at lower pressure than the column. The performance of three types of fixed flow restrictor, the “tapered”, the “integral”, and the “frit”, was examined. The test mixtures chosen covered a range of polarities and molecular weights. Polydimethylsiloxane with an average molecular weight of 10,000 was used as a low polarity probe. Two polyethylene glycol mixtures were chosen as higher polarity probes. One consisted of a mixture of polyethylene glycol standards with average molecular weights ranging from 200 to 1450. The other polyethylene glycol mixture had an average molecular weight of 2000. The polydimethylsiloxane standard did not elute when the frit restrictor was used. Satisfactory results were obtained when the tapered and integral restrictors were employed. All three restrictors provided satisfactory results for polyethylene glycol oligomers eluting up to approximately 40.5 MPa (400 atm). However, for oligomers eluting above this pressure, the peaks merged into a broad hump with the frit restrictor, while the tapered and integral restrictors provided satisfactory separations. The integral restrictor produced more evenly spaced, more well resolved peaks at the high-pressure end of the chromatograms than did the tapered restrictor. This is shown to be due to differences in the rates of increase in mobile-phase velocity with increasing pressure for the two restrictors.     

Low-level laser therapy promotes vascular endothelial growth factor receptor-1 expression in endothelial and nonendothelial cells of mice gastrocnemius exposed to snake venom

Crotalinae snake venoms cause severe local myonecrosis and microvasculature failure at the bite site. We evaluated whether low-level laser therapy (LLLT) could accelerate angiogenesis and myoregeneration in male Swiss mice injected with Bothrops moojeni venom through immunohistochemistry of the vascular endothelial growth factor receptor-1 (VEGFR-1). Envenomed gastrocnemius was either unirradiated (V) or irradiated with HeNe (VHN, 632.8 nm) or GaAs (VGA, 904 nm, 10000 Hz). Animals sacrificed at 3 and 12 h were irradiated once (4 J cm(-2)), at 24 h (twice) and at 3, 7, 21 days (4, 8, 22 times, respectively). At 3 days, LLLT increased angiogenesis (80%:HeNe vs 40%:GaAs), decreased neutrophils and increased proliferation of regenerating cells. However, after 21 days, myoregeneration observed in the VHN group appeared delayed compared with the V group. As LLLT improved revascularization, the suggestive delay in myoregeneration could be a dose-response inhibitory effect caused by multiple irradiations in myogenesis. The immunodetection of VEGFR-1 in neutrophils, macrophages, satellite cells, fibroblasts, Schwann cells and skeletal and smooth muscle fibers (not seen in saline-controls) at only the acute stages of envenoming suggests a mediator role for VEGFR-1 in local alterations. This is the first time that VEGFR-1 expression, and its modulation by photostimulation, has been demonstrated in endothelial and nonendothelial cells of snake envenomed skeletal muscle.