Biochemistry

Two types of short double-stranded RNA molecules, namely microRNAs (miRNAs) and short interfering RNAs (siRNAs), have emerged recently as important regulators of gene expression. Although these molecules show similar sizes and structural features, the mechanisms of action underlying their respective target silencing activities appear to differ: siRNAs act primarily through mRNA degradation, whereas most miRNAs appear to act primarily through translational inhibition. Our understanding of how these overlapping pathways are differentially regulated within the cell remains incomplete. In the present work, quantitative fluorescence microscopy was used to study how siRNAs are processed within human cells. We found that siRNAs are excluded from non-nucleolar areas of the nucleus in an Exportin-5 dependent process that specifically recognizes key structural features shared by these and other small RNAs such as miRNAs. We further established that the Exportin-5-based exclusion of siRNAs from the nucleus can, when Exp5 itself is inhibited, become a rate-limiting step for siRNA-induced silencing activity. Exportin 5 therefore represents a key point of intersection between the siRNA and miRNA pathways, and, as such, is of fundamental importance for the design and interpretation of RNA interference experimentation.

It has been proposed that cytoskeletal elements including actin and microtubules are involved in facilitating the propagation of electrical signals in the cell (see [1, 2] for an indepth discussion). Priel et al.[3] experimentally demonstrated that microtubules are excellent conductors of electrical signals and can amplify an electrical current stimulated by a pulse of applied voltage. The current collected 20–50 m further down the microtubule (MT) was found to be double its value in the buffer solution with no MT present.

The topological control hypothesis presented by Bostick and Brooks [Proc. Natl. Acad. Sci. USA 2007, 104, 9260] has sought to explain binding selectivity in potassium channels based on the premise that a universal measure of ion solvation in different environments is provided by its average coordination structure in bulk water. This leads to the view that ion selectivity is predominantly controlled by the number of ligands coordinating the ion and that the chemical type of those ligands plays a minor role.

A theoretical framework is presented to model ion and DNA translocation across a nanopore confinement under an applied electric field. A combined Grand Canonical Monte Carlo Brownian Dynamics (GCMC/BD) algorithm offers a general approach to study ion permeation through wide molecular pores with a direct account of ion–ion and ion–DNA correlations.