Thermodynamics of formation of nitrogen bases and d-ribose from mineral substances in light of the problem of origination of simplest elements of living matter

The paper represents a further development of our hydrate hypothesis of simplest living matter origination (SLMO) from inorganic and simplest organic mineral substances. It is supposed that the sources of SLMO are simplest aliphatic hydrocarbons, niters, and phosphates. Thermodynamic calculations demonstrating a principal possibility for simultaneous syntheses of different nitrogen bases, d-ribose, and desoxy-d-ribose from these source substances are presented. The most probable principal mechanism of SLMO and the principal conditions necessary for realization of the proposed chemism of SLMO in the framework of the proposed mechanism are considered. A principal means for testing the hypothesis is proposed.     

Solid-state,optical-rotation measurements on macromolecules using powder-suspensions

Summary We report techniques for measuring optical rotation of suspended solids, including dissymmetric molecular crystals (e.g. sodium chlorate and bromate), synthetic polymers, polypeptides and biopolymers. Examples include poly(triphenylmethyl methacrylate), poly-S-lactide, poly-L-hydroxyproline, hemocyanine, cellulose acetate andRNA. The results indicate that optical rotation measurements are sensitive to differences in secondary structure and can serve as a probe for structural differences between solid-state and solution.

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Messung der optischen Rotation von Makromolekülen im Festzustand unter Verwendung von Pulversuspensionen

Zusammenfassung Es wird über eine Methode zur Messung der optischen Rotation von Festkörpern in Suspensionen berichtet, wobei dissymetrische Kristalle (z. B. Natriumchlorat und -bromat), synthetische Polymere, Polypeptide und Biopolymere behandelt werden. Die Beispiele umfassen Poly(triphenylmethylmethacrylat), Poly-S-lactid, Poly-L-hydroxyprolin, Hemocyanin, Celluloseacetat undRNA. Die Ergebnisse zeigen, daß die optischen Rotationen bezüglich Unterschiede in der Sekundärstruktur empfindlich sind und daß diese Messungen als ein Maß für Strukturunterschiede zwischen Festzustand und Lösung herangezogen werden können.

     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

Stochastic detection of motor protein-RNA complexes by single-channel current recording.

A label- and immobilization-free approach to detecting the reversible formation of complexes between nucleic acids and proteins at the single-molecule level is described. The voltage-driven translocation of individual oligoribonucleotides through a nanoscale protein pore is observed by single-channel current recordings. The oligoribonucleotide 5'-C25A(25)-3' gives rise to current blockades with an average duration of approximately 0.5 ms. In the presence of the RNA-binding ATPase P4, a viral packaging motor from bacteriophage phi8, longer events of tens to hundreds of milliseconds are observed. Upon addition of ATP the long events disappear, indicating the dissociation of the P4RNA complex. The frequency of events also depends on the concentration of P4 and the length of the oligoribonucleotide, thereby confirming the specificity of the P4RNA events. This study shows that single-channel current recordings can be used to monitor RNA-protein complex formation, thus opening up a new means to examine the motor activity of RNA- or DNA-processing enzymes.     

Vesicle formation between single-chained cationic surfactants and ribo-oligonucleotides

Recently,we reported that deoxyribo-oligonucleotides could induce single chained cationic surfactant aggregation to form vesicles.In this paper,we will present that ribo-oligonucleotides can also induce vesicle formation,and compared with deoxyribo-oligonucleotides,ribo-oligonucleotides exhibit a higher inductive efficiency.