Corrected Mean-Field Model for Random Sequential Adsorption on Random Geometric Graphs

A notorious problem in mathematics and physics is to create a solvable model for random sequential adsorption of non-overlapping congruent spheres in the d-dimensional Euclidean space with \(d\ge 2\). Spheres arrive sequentially at uniformly chosen locations in space and are accepted only when there is no overlap with previously deposited spheres. Due to spatial correlations, characterizing the fraction of accepted spheres remains largely intractable. We study this fraction by taking a novel approach that compares random sequential adsorption in Euclidean space to the nearest-neighbor blocking on a sequence of clustered random graphs. This random network model can be thought of as a corrected mean-field model for the interaction graph between the attempted spheres. Using functional limit theorems, we characterize the fraction of accepted spheres and its fluctuations.     

Long strange segments,ruin probabilities and the effect of memory on moving average processes

We obtain the rate of growth of long strange segments and the rate of decay of infinite horizon ruin probabilities for a class of infinite moving average processes with exponentially light tails. The rates are computed explicitly. We show that the rates are very similar to those of an i.i.d. process as long as the moving average coefficients decay fast enough. If they do not, then the rates are significantly different. This demonstrates the change in the length of memory in a moving average process associated with certain changes in the rate of decay of the coefficients.     

Antagomirzymes: Oligonucleotide Enzymes That Specifically Silence MicroRNA Function

Many important cellular processes are regulated by small endogenous noncoding RNAs known as microRNAs (miRNAs). The precise molecular function of many miRNAs is unknown; different loss‐of‐function methods are required to gain insight into the biology of these small RNA molecules. Nucleic acid enzymes termed antagomirzymes are now shown to be valuable tools for the specific knockdown of miRNA in vitro and in vivo (see scheme).

     

Oxo transfer reaction: Dioxido and monooxidovanadium(V) complexes

A dioxidovanadium(V) complex of type [(L_ONOH^?)(VO₂)] (1) was isolated where L_ONOH₂ is a tridentate ONO donor benzhydrazide ligand. 1 undergoes an oxo transfer reaction with triphenylphosphine in presence of 8-hydroxyquinoline (HQ) and affords a monooxidovanadium(V) complex of type [(L_ONO^2?)(VO)(Q^?)] (2). 1 and 2 were substantiated by elemental analyses, ESI-mass, IR, ¹H NMR, ⁵¹V NMR and UV–vis spectra. The molecular geometries of 1 and 2 were authenticated by single crystal X?ray crystallography. UV–vis absorption spectra of 1 and 2 display bands respectively at 325 and 320 nm due to oxido → vanadium(V) charge transfer transitions. 1 exhibit an irreversible cathodic peak at ?0.44 V whereas 2 displays a reversible cathodic wave at ?0.60 V in cyclic voltammogram due to the VO³⁺/VO²⁺ redox couple.     

Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting

Recent advances in proteomics have provided impetus towards the development of robust technologies for high-throughput studies of enzymes. The term “catalomics” defines an emerging ‘-omics’ field in which high-throughput studies of enzymes are carried out by using advanced chemical proteomics approaches. Of the various available methods, microarrays have emerged as a powerful and versatile platform to accelerate not only the functional annotation but also the substrate and inhibitor specificity (e.g. substrate and inhibitor fingerprinting, respectively) of enzymes. Herein, we review recent developments in the fabrication of various types of microarray technologies (protein-, peptide- and small-molecule-based microarrays) and their applications in high-throughput characterizations of enzymes.     

Energetics of the human Tel-22 quadruplex-telomestatin interaction: a molecular dynamics study

The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadruplex as an attractive target for cancer therapeutic intervention. In this context, telomestatin, a G-quadruplex-specific ligand known to bind and stabilize G-quadruplex, is of great interest. Knowledge of the three-dimensional structure of telomeric quadruplex and its complex with telomestatin in solution is a prerequisite for structure-based rational drug design. Here, we report the relative stabilities of human telomeric quadruplex (AG3[T2AG3]3) structures under K+ ion conditions and their binding interaction with telomestatin, as determined by molecular dynamics simulations followed by energy calculations. The energetics study shows that, in the presence of K+ ions, mixed hybrid-type Tel-22 quadruplex conformations are more stable than other conformations. The binding free energy for quadruplex-telomestatin interactions suggests that 1:2 binding is favored over 1:1 binding. To further substantiate our results, we also calculated the change in solvent-accessible surface area (DeltaSASA) and heat capacity (DeltaCp) associated with 1:1 and 1:2 binding modes. The extensive investigation performed for quadruplex-telomestatin interaction will assist in understanding the parameters influencing the quadruplex-ligand interaction and will serve as a platform for rational drug design.