Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopy.

The protocol described in this chapter allows for acquiring topography images of RNA-based nanoring structures and assessing their dynamic properties using atomic force microscopy (AFM) imaging. AFM is an indispensable tool for characterization of nucleic acid-based nanostructures with the exceptional capability of observing complexes in the range of a few nanometers. This method can visualize structural characteristics and evaluate differences between individual structurally different RNA nanorings.

The non-canonical mechanism of ER stress-mediated progression of prostate cancer.

Background: The development of persistent endoplasmic reticulum (ER) stress is one of the cornerstones of prostate carcinogenesis; however, the mechanism is missing. Also, alcohol is a physiological ER stress inducer, and the link between alcoholism and progression of prostate cancer (PCa) is well documented but not well characterized. According to the canonical model, the mediator of ER stress, ATF6, is cleaved sequentially in the Golgi by S1P and S2P proteases; thereafter, the genes responsible for unfolded protein response (UPR) undergo transactivation.

Tuning properties of silver nanoclusters with RNA nanoring assemblies.

Combining atomically resolved DNA-templated silver nanoclusters (AgNCs) with nucleic acid nanotechnology opens new exciting possibilities for engineering bioinorganic nanomaterials with uniquely tunable properties. In this unforeseen cooperation, nucleic acids not only drive the formation of AgNCs but also promote their spatial organization in supra-assemblies. In this work, we confirm the feasibility of this approach using programmable RNA rings to control formation and optical properteis of six individual AgNCs.

Cyclization in bipartite random graphs.

In this paper the time evolution of a finite bipartite graph initially comprising two sorts of isolated vertices is considered. The graph is assumed to evolve by adding edges, one at a time. Each new edge connects either two linked components and forms a new component of a larger order (coalescence of graphs) or increases (by one) the number of edges in a given linked component (cycling).

Post-ER Stress Biogenesis of Golgi Is Governed by Giantin.

Background: The Golgi apparatus undergoes disorganization in response to stress, but it is able to restore compact and perinuclear structure under recovery. This self-organization mechanism is significant for cellular homeostasis, but remains mostly elusive, as does the role of giantin, the largest Golgi matrix dimeric protein.

Methods: In HeLa and different prostate cancer cells, we used the model of cellular stress induced by Brefeldin A (BFA).