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.     

Biochemical sensors: The state of the art

The basic components of a (bio)chemical sensor and the main concepts involved in the (bio)chemical sensor methodology are considered in order to depict the state of the art of the development of research in this field, paying special attention to the evolution of the published scientific literature in analytical chemistry.     

An observation on the effect of fluctuations far from equilibrium: The Lotka-Volterra model

Spontaneous fluctuations in the Lotka-Volterra model of chemical reactions are known to grow in an unbounded way when species held in excess are neglected. This result is obtained in a simple way using generalized fluctuation-dissipation principles but appears to be an artifact of ignoring fluctuations in the variables that are held fixed. When fluctuations in the other concentrations are included in the model, the spontaneous fluctuations become bounded.This work was supported by the National Science Foundation through Research Grant No. MPS 74-00483 AO1.     

Generalized nonlinear master equations for local fluctuations: Dimensionality expansions and augmented mean field theory

By application of a projection operator technique we derive a formally exact generalization of the nonlinear mean field master equation introduced recently for the study of local fluctuations in a reacting medium. Our starting point is a phenomenological cell master equation. The results of our theory are applicable to the theory of a fluctuating hydrodynamic reacting system. The mean field equation is placed on a firm theoretical foundation by showing it to be the lowest order approximation in an expansion in the dimensionality of the physical space keeping the product of the number of nearest neighbors (an increasing function of dimensionality) and the typical diffusion coefficient constant. A more accurate nonlinear master equation that allows for the correlation and fluctuations in the environment of a given volume element is derived in the form of an augmented mean field equation.Work supported in part by a grant from the National Science Foundation.     

Unfolding Features of Bovine Testicular Hyaluronidase Studied by Fluorescence Spectroscopy and Fourier Transformed Infrared Spectroscopy

Chemical unfolding of bovine testicular hyaluronidase (HAase) has been studied by fluorescence spectroscopy and Fourier transformed infrared spectroscopy (FTIR). Thermodynamic parameters were determined for unfolding HAase from changes in the intrinsic fluorescence emission intensity and the formations of several possible unfolding intermediates have been identified. This was further confirmed by representation of fluorescence data in terms of ‘phase diagram’. The secondary structures of HAase have been assigned and semiquantitatively estimated from the FTIR. The occurrence of conformational change during chemical unfolding as judged by fluorescence and FTIR spectroscopy indicated that the unfolding of HAase may not follow the typical two-state model.     

Bonding in [CuNRR’]<Subscript>4</Subscript> type clusters

Many polynuclear Cu(I) compounds have been synthesized, but the problem whether there is direct or no direct Cu-Cu bonding in these compounds is not clear. The electronic structure of [CuNRR’]₄ type clusters was investigated by using density functional methods. The results of geometrical optimization are in good agreement with experiment, and the localization of MO’s shows that there are four Cu-Cu σ bonds to form the square Cu₄ ring in addition to the four bridging Cu-N-Cu bonds. A concept of the covalence of molecular fragments is proposed to describe the bonding in these clusters.     

Random coil phosphorus chemical shift of deoxyribonucleic acids

Random coil phosphorus chemical shift has been studied using 16 17-nucleotide DNA sequences. Due to the presence of residual base stacking in these sequences, the temperature and sequence effects were investigated at 50 and 55 degrees C. The phosphorus chemical shifts of random coil DNA sequences have been found to be independent of temperature. Sequence effect analysis shows that the phosphorus chemical shift of a nucleotide in a random coil DNA sequence depends on both its 5'- and 3'-nearest neighbors. A trimer model has been used to establish the random coil 31P chemical shift prediction protocol which shows an accuracy of 0.02 ppm.