Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

Background: The translation or stability of the mRNAs from ferritin, m-aconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of higher-solution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms.Results: Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern.Conclusions: The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes, The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.     

Vibrational-translational/rotational and vibrational-vibrational processes in methane/inert-gas mixtures: Optoacoustic phase measurements

We consider the model with kinetic excitation into the quasicontinuum (KEQ) for resonant polyatomic molecules which absorb laser radiation and are surrounded by buffer molecules. KEQ takes place when the resonant molecules in the lower part of the energy spectrum interact weakly with the laser radiation, but the molecules in the quasicontinuum are rapidly excited to still higher energy and dissociate. Under these conditions the collisions of the resonant and buffer molecules lead to excitation of resonant molecules into the quasicontinuum because the population of the quasicontinuum is much less than its thermodynamical equilibrium value. It is found, that the smaller the V-T relaxation time τ_VT, the larger the rate of KEQ and the dissociation rate (if only τ_VT is not too small). Thus, if we change the experimental conditions and decrease τ_VT (for instance, by passing from the heavy buffer gas Xe to the light buffer gas He), for some resonant molecules we may observe that the probability of dissociation increases.     

Pattern recognition display methods for the analysis of computed molecular properties

Summary Pattern recognition methods, particularly the unsupervised learning techniques, are well suited for the preliminary analysis of the large data sets produced by computer chemistry. The use of linear and non-linear display methods for such exploratory analysis are exemplified with the aid of two data sets of biologically active molecules. Advantages and disadvantages of these techniques are discussed.     

Photo-oxidation of unsaturated ferrocenyl-substituted carboxylic acids

In aqueous solution (pH 9) containing N₂O, the unsaturated acids $\text{trans}$-FcCHCH(CH₂)nCO₂H (n = 0 and 1) and FcCCCO₂H each undergo photo-oxidation, upon illumination with u.v. light of wavelength 240-250 nm, giving dipolar ferricenium species which may be chemically reduced back to the original acids. The mechanism of photo-oxidation, which is inhibited by ethanol, appears to be similar to that previously proposed for saturated ω-ferrocenylalkanoic acids.     

Photochemically induced electron transfer from [3]ferrocenophanylbutanoate anions

The anions of 4-([3]ferrocenophanyl)butanoic acids (Id and IId), when excited by light of around 240 nm wavelength in aqueous solution in the presence of N₂O, undergo photo-oxidation to zwitterions (III and IV respectively) in a manner completely analogous to the reaction of 4-ferrocenylbutanoate anion. The differences in the kinetic parameters of the reactions are thought to be attributable in part to slight tilting of the cyclopentadienyl rings caused by the connecting trimethylene bridge.     

Self-assembling porphyrin-modified peptides

[structure: see text] We report the synthesis and characterization of a novel supramolecular assembly that features long-range electronic coupling between porphyrins covalently attached to a designed peptide scaffold. The resulting construct self-assembles to form extended organized aggregates in which the porphyrins engage in exciton coupling.     

Sound radiation around a flying fly

Many insects produce sounds during flight. These acoustic emissions result from the oscillation of the wings in air. To date, most studies have measured the frequency characteristics of flight sounds, leaving other acoustic characteristics--and their possible biological functions--unexplored. Here, using close-range acoustic recording, we describe both the directional radiation pattern and the detailed frequency composition of the sound produced by a tethered flying (Lucilia sericata). The flapping wings produce a sound wave consisting of a series of harmonics, the first harmonic occurring around 190 Hz. In the horizontal plane of the fly, the first harmonic shows a dipolelike amplitude distribution whereas the second harmonic shows a monopolelike radiation pattern. The first frequency component is dominant in front of the fly while the second harmonic is dominant at the sides. Sound with a broad frequency content, typical of that produced by wind, is also recorded at the back of the fly. This sound qualifies as pseudo-sound and results from the vortices generated during wing kinematics. Frequency and amplitude features may be used by flies in different behavioral contexts such as sexual communication, competitive communication, or navigation within the environment.     

The temporal effect in listeners with mild to moderate cochlear hearing impairment

This study examines the relationship between a temporal masking effect and cochlear hearing impairment. The threshold level of a long-duration broadband masker needed to mask a short-duration tonal signal was measured for signals presented 2 ms (short-delay) or 202 ms (long-delay condition) after masker onset. The difference between these thresholds is the temporal effect. In two previous studies with normal-hearing listeners, estimates of gain of the cochlear active process derived from such data suggested a decrease in gain during the course of the masker. This hypothesis was further examined in the present study by testing listeners with mild to moderate cochlear hearing impairment. Results are consistent with a decrease in gain in the short-delay condition with increasing hearing impairment, and also less change in gain with increasing hearing impairment.