Direct Determination of the Structure of Single Biopolymer Molecules Using Nanopore Sequencing

This review highlights operational principles, features, and modern aspects of the development of third-generation sequencing technology of biopolymers focusing on the nucleic acids analysis, namely the nanopore sequencing system. Basics of the method and technical solutions used for its realization are considered, from the first works showing the possibility of creation of these systems to the easy-to-handle procedure developed by Oxford Nanopore Technologies company. Moreover, this review focuses on applications, which were developed and realized using equipment developed by the Oxford Nanopore Technologies, including assembly of whole genomes, methagenomics, direct analysis of the presence of modified bases.

Self-organization of cationic dendrimers in polyanionic hydrogels

Protonated poly(propylene imine) dendrimers (Astramol) of five generations: DAB-dendr-(NH2)x (where x=4, 8, 16, 32 or 64) are sorbed by slightly cross-linked polyanionic hydrogels: poly(sodium acrylate) and poly(sodium 2-acrylamido-2-methylpropane sulfonate). As a result highly swollen original hydrogel transforms into compact cross-linked polyelectrolyte-dendrimer complexes. Sorption of dendrimers by the hydrogels is a chemically drawn frontal diffusion process. Driving force comes from the gain in the free energy of interpolyelectrolyte coupling reaction between the charged dendrimer molecules and the oppositely charged hydrogel network, accompanied with entropically favourable release of low molecular salt into environment. The amount of a simple salt released is equivalent to a number of intermolecular salt bonds, formed between protonated dendrimers and hydrogel networks. Apparently the mechanism of dendrimer uptake involves a "relay-race" transfer of dendrimer polycations from one fragment of polyelectrolyte network to the other via interpolyelectrolyte exchange reaction. As a result "core-shell" constructs consisting of outer weakly swollen complex shell and highly swollen hydrogel core are formed at intermediate stages of the process. The rate of sorption is determined by the rate of the interpolyelectrolyte exchange reaction that is the rate of the formation of free fragments of polyelectrolyte network (vacancies) on the inner complex-hydrogel boundary. The amount of vacancies depends on the area of this boundary. Consequently kinetics of dendrimer uptake could not be fitted in terms of Fickian diffusion (except DAB-dendr-(NH2)4), but expressed in terms of the kinetic equation derived for a frontal heterogeneous reaction. Sorbed dendrimers of all studied generations at pH values ensuring complete protonation of primary and tertiary amine groups are closely packed in hydrogel networks, so that all dendrimer cationic units form ion pairs with anionic units of hydrogels. In other words polyanionic network fragments are able to penetrate into the interior of fully protonated DAB-dendr-(NH2)x species as it was earlier shown for flexible linear polyanions. In such case the ultimate amount of sorbed dendrimer molecules is always determined by the condition n(a)/N- = 1, where n(a) is the total number of dendrimer amine groups, N- is the number of the anionic hydrogel units. The latter is also true for the complex shell composition in the heterogeneous reacting samples formed at intermediate stages of dendrimers uptake. Variation of pH and sorption extent is an effective tool to control dendrimer distribution, self-organization and the final structure of dendrimer-hydrogel constructs.