Targeting the A site RNA of the Escherichia coli ribosomal 30 S subunit by 2'-O-methyl oligoribonucleotides: a quantitative equilibrium dialysis binding assay and differential effects of aminoglycoside antibiotics.

The bacterial ribosome comprises 30 S and 50 S ribonucleoprotein subunits, contains a number of binding sites for known antibiotics and is an attractive target for selection of novel antibacterial agents. On the 30 S subunit, for example, the A site (aminoacyl site) close to the 3'-end of 16 S rRNA is highly important in the decoding process. Binding by some aminoglycoside antibiotics to the A site leads to erroneous protein synthesis and is lethal for bacteria. We targeted the A site on purified 30 S ribosomal subunits from Escherichia coli with a set of overlapping, complementary OMe (2'-O-methyl) 10-mer oligoribonucleotides. An equilibrium dialysis technique was applied to measure dissociation constants of these oligonucleotides. We show that there is a single high-affinity region, spanning from A1493 to C1510 (Kd, 29-130 nM), flanked by two lower-affinity regions, within a span from U1485 to G1516 (Kd, 310-4300 nM). Unexpectedly, addition of the aminoglycoside antibiotic paromomycin (but not hygromycin B) caused a dose-dependent increase of up to 7.5-fold in the binding of the highest affinity 10-mer 1493 to 30 S subunits. Oligonucleotides containing residues complementary to A1492 and/or A1493 showed particularly marked stimulation of binding by paromomycin. The results are consistent with high-resolution structures of antibiotic binding to the A site and with greater accessibility of residues of A1492 and A1493 upon paromomycin binding. 10-mer 1493 binding is thus a probe of the conformational switch to the 'closed' conformation triggered by paromomycin that is implicated in the discrimination by 30 S subunits of cognate from non-cognate tRNA and the translational misreading caused by paromomycin. Finally, we show that OMe oligonucleotides targeted to the A site are moderately good inhibitors of in vitro translation and that there is a limited correlation of inhibition activity with binding strength to the A site.

The geometric factor of electrostatic plasma analyzers: a case study from the Fast Plasma Investigation for the Magnetospheric Multiscale mission.

We report our findings comparing the geometric factor (GF) as determined from simulations and laboratory measurements of the new Dual Electron Spectrometer (DES) being developed at NASA Goddard Space Flight Center as part of the Fast Plasma Investigation on NASA's Magnetospheric Multiscale mission. Particle simulations are increasingly playing an essential role in the design and calibration of electrostatic analyzers, facilitating the identification and mitigation of the many sources of systematic error present in laboratory calibration. While equations for laboratory measurement of the GF have been described in the literature, these are not directly applicable to simulation since the two are carried out under substantially different assumptions and conditions, making direct comparison very challenging. Starting from first principles, we derive generalized expressions for the determination of the GF in simulation and laboratory, and discuss how we have estimated errors in both cases. Finally, we apply these equations to the new DES instrument and show that the results agree within errors. Thus we show that the techniques presented here will produce consistent results between laboratory and simulation, and present the first description of the performance of the new DES instrument in the literature.