Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides,m(3)Psi and Psi

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.     

Entropic barriers in nanoscale adhesion studied by variable temperature chemical force microscopy

Intermolecular interactions drive the vast majority of condensed phase phenomena from molecular recognition to protein folding to particle adhesion. Complex energy barriers encountered in these interactions include contributions from van der Waals forces, hydrogen bonding, and solvent medium. With the spectacular exception of hydrophobic interactions, contributions from the medium are usually considered secondary. We report a variable temperature force microscopy study of the interactions between several hydrogen bonds in different solvents that challenges this point of view. Surprisingly, we observed an increase in the strength of the interaction between carboxylic acid groups in ethanol as the temperature increased. Moreover, when we switched to a nonpolar solvent we observed the opposite behavior: The binding force decreased as the temperature increased. Kinetic model of bond dissociation provided quantitative interpretation of our measurements. We attributed the observed phenomena to a large entropic contribution from the ordered solvent layers that are forming on the probe and sample surfaces upon detachment. The observed reversal in the force vs temperature trend is a manifestation of a transition between thermodynamic and kinetic regimes of unbinding predicted by the model. Our results indicate that entropic barriers dominated by the interactions of solvent molecules with the surface exist in a much wider variety of systems than previously thought.     

Photoinduced axial ligation and deligation dynamics of nonplanar nickel dodecaarylporphyrins

The ground- and excited-state metal-ligand dynamics of nonplanar nickel(II) 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (NiDPP) and two fluorinated analogues (NiF(20)DPP and NiF(28)DPP) have been investigated using static and time-resolved absorption spectroscopy in toluene and in ligating media that differ in basicity, aromaticity, and steric encumbrance. Because of the electronic and steric consequences of nonplanarity, NiDPP does not bind axial ligands in the ground state, but metal coordination does occur after photoexcitation with multistep dynamics that depend on the properties of the ligand. Following the structural relaxations that occur in all nickel porphyrins within approximately 10 ps, ligand binding to photoexcited NiDPP is progressively longer in pyridine, piperidine, and 3,5-lutidine (25-100 ps) but does not occur at all in 2,6-lutidine in which the ligating nitrogen is sterically encumbered. The transient intermediate that is formed, which nominally could be either a five- or six-coordinate species, also has a ligand-dependent lifetime (200-550 ps). Decay of this intermediate occurs partially via ligand release to re-form the uncoordinated species, in competition with binding of the second axial ligand and/or conformational/electronic relaxations (of a six-coordinate intermediate) to give the ground state of the bis-ligated photoproduct. The finding that the photoproduct channel principally depends on ligand characteristics along with the time-evolving spectra suggests that the transient intermediate may involve a five-coordinate species. In contrast to NiDPP, the fluorinated analogues NiF(20)DPP and NiF(28)DPP do coordinate axial ligands in the ground state but eject them after photoexcitation. Collectively, these results demonstrate the sensitivity with which the electronic and structural characteristics of the macrocycle, substituents, and solvent (ligands) can govern the photophysical and photochemical properties of nonplanar porphyrins and open new avenues for exploring photoinduced ligand association and dissociation behavior.     

Synthesis of 15N-enriched pseudouridine derivatives

[reaction: see text]. A procedure for the chemical synthesis of [3-15N]-labeled pseudouridine and a methylated derivative was developed. A suitably protected pseudouridine precursor was nitrated at N3 followed by treatment with 15NH4Cl to afford the 15N-labeled product in six steps with a 20% yield. This methodology will allow for the production of RNAs with [3-15N]pseudouridine and [3-15N-methyl]pseudouridine at specific locations.     

Separation of Aliphatic and Aromatic Carboxylic Acids by Conventional and Ultra High-Performance Ion-Exclusion Chromatography

An ion-exclusion chromatography (IELC) comparison between a conventional ion-exchange column and an ultra high-performance liquid chromatography (UHPLC) dynamically surfactant modified C18 column for the separation of an aliphatic carboxylic acid and two aromatic carboxylic acids is presented. Professional software is used to optimize the conventional IELC separation conditions for acetylsalicylic acid and the hydrolysis products: salicylic acid and acetic acid. Four different variables are simultaneously optimized including H₂SO₄ concentration, pH, flow rate, and sample injection volume. Thirty different runs are suggested by the software. The resolutions and the time of each run are calculated and feed back to the software to predict the optimum conditions. Derringer’s desirability functions are used to evaluate the test conditions and those with the highest desirability value are utilized to separate acetylsalicylic acid, salicylic acid, and acetic acid. These conditions include using a 0.35 mM H₂SO₄ (pH 3.93) eluent at a flow rate of 1 mL min^?1 and an injection volume of 72 μL. To decrease the run time and improve the performance, a UHPLC C18 column is used after dynamic modification with sodium dodecyl sulfate. Using pure water as a mobile phase, a shorter analysis time and better resolution are achieved. In addition, the elution order is different from the IELC method which indicates the contribution of the reversed-phase mode to the separation mechanism.     

Integrated biological–chemical approach for the isolation and selection of polyaromatic mutagens in surface waters

Many environmental mutagens, including polyaromatic compounds are present in surface waters, often in complex mixtures and at low concentrations. The present study provides and applies a novel, integrated approach to isolate polyaromatic mutagens in river water using a sample from the River Elbe. The sample was taken downstream of industrial discharges using blue rayon (BR) as a passive sampler that selectively adsorbs polyaromatic compounds and was subjected to effect-directed fractionation in order to characterise the compounds causing the detected effect(s). The procedure relies on three complementary fractionation steps, the Ames fluctuation assay with strains TA98, YG1024 and YG1041 with and without S9 activation and analytical screening. Several mutagenic fractions were isolated by combining mutagenicity testing with fractionation. The enhanced mutagenicity in the nitroreductase and/or O-acetyltransferase overexpressing strains YG1024 and YG1041 strains suggested amino- and/or nitro-compounds causing mutagenicity in several fractions. Analytical screening of mutagenic fractions with LC-HRMS/MS provided a list of molecular formulas typically containing one to ten nitrogen and at least two oxygen atoms supporting the presence of amino and nitro-compounds in the mutagenic fractions.