Design and synthesis of artificial ribonucleases based on 1,4-diazabicyclo[2.2.2]octane and imidazole

The review surveys the results of our studies devoted to the design of highly efficient catalysts of hydrolysis of the phosphodiester bonds in RNA. These catalysts contain the imidazole residue in the catalytic domain, one or several bis-quaternized rings of 1,4-diazabicyclo[2.2.2]octane as a polycationic RNA-binding domain, and a lipophilic radical. A versatile approach to artificial ribonucleases of this type was proposed, which allows one to vary not only the number of positive charges in the RNA-binding domain, the structure of the catalytic site, and their mutual arrangement but also the domain structure of the molecule as a whole. Analysis of the catalytic properties of the synthesized constructs makes it possible to optimize the domain structure and the geometry of the molecule ensuring its maximum ribonuclease activity.     

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.     

Statistical theory of force-induced unzipping of DNA

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force F_c(T) for unzipping calculated in the constant force ensemble is found to depend on the potential parameter k which measures the stiffness associated with a single strand of DNA and on D, the well depth of the on-site potential representing the strength of hydrogen bonds in a base pair. The dependence on temperature of F_c(T) is found to be (T_D - T)^1/2 (T_D being the thermal denaturation temperature) with F_c(T_D) = 0 and F_c(0) = . We used the constant extension ensemble to calculate the average force F(y) required to stretch a base pair a y distance apart. The value of F(y) needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance for y 1.0 . The force F(y) in both cases is found to have a very large value for y 0.2 compared to the critical force found from the constant force ensemble to which F(y) approaches for large values of y. It is shown that the value of F(y) at the peak depends on the value of k which measures the energy barrier associated with the reduction in DNA strand rigidity as one passes from dsDNA to ssDNA and on the value of the depth of the on-site potential. The effect of defects on the position and height of the peak in the F(y) curve is investigated by replacing some of the base pairs including the one being stretched by defect base pairs. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of an eye when a base pair far from ends is stretched are investigated.     

Effect of spermine and DNase on DNA release from bacteriophage T5

Bacterial viruses (bacteriophages) consist of nucleic acid protected by a protein envelope called capsid. At the start of infection, the phage genome is translocated into the bacterial cytoplasm. In vitro (and also in vivo), this DNA release can be triggered by binding a specific receptor protein to the phage tail. The force responsible for the release arises from energy stored in the capsid due to strong confinement of the DNA. We show that this force can be modified by adding molecules like spermine that affect DNA conformation. The tetravalent cation spermine can reduce the pressure inside the capsid and induce condensation of the released DNA. We examine the effect of spermine on DNA ejection from phage T5 by using light scattering and gel electrophoresis to measure the amount of DNA remaining in the capsid at the end of ejection. We discuss the results in terms of free energy minimization and we demonstrate that the presence of a DNA condensate outside the phage generates an additional force pulling passively on the DNA remaining inside the capsid.     

Aminoglycoside microarrays to explore interactions of antibiotics with RNAs and proteins

RNA is an important target for drug discovery efforts. Several clinically used aminoglycoside antibiotics bind to bacterial rRNA and inhibit protein synthesis. Aminoglycosides, however, are losing efficacy due to their inherent toxicity and the increase in antibiotic resistance. Targeting of other RNAs is also becoming more attractive thanks to the discovery of new potential RNA drug targets through genome sequencing and biochemical efforts. Identification of new compounds that target RNA is therefore urgent, and we report here on the development of rapid screening methods to probe binding of low molecular weight ligands to proteins and RNAs. A series of aminoglycosides has been immobilized onto glass microscope slides, and binding to proteins and RNAs has been detected by fluorescence. Construction and analysis of the arrays is completed by standard DNA genechip technology. Binding of immobilized aminoglycosides to proteins that are models for study of aminoglycoside toxicity (DNA polymerase and phospholipase C), small RNA oligonucleotide mimics of aminoglycoside binding sites in the ribosome (rRNA A-site mimics), and a large (approximately 400 nucleotide) group I ribozyme RNA is detected. The ability to screen large RNAs alleviates many complications associated with binding experiments that use isolated truncated regions from larger RNAs. These studies lay the foundation for rapid identification of small organic ligands from combinatorial libraries that exhibit strong and selective RNA binding while displaying decreased affinity to toxicity-causing proteins.