Asymmetric bridging of interconnected pores by encased semiflexible macromolecules

Conformation of Flexible and Semiflexible Chains Confined in Nanoposts Array of Various Geometries

The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulations. The geometry of the nanopost array was varied at the constant post diameter dp and the ensuing modifications of the chain conformation were compared with the structural behavior of the chain in the series of nanopost arrays with the constant post separation Sp as well as with the constant distance between two adjacent post walls (passage width) wp. The free energy arguments based on an approximation of the array of nanopost to a composite of quasi-channels of diameter dc and quasi-slits of height wp provide semiqualitative explanations for the observed structural behavior of both chains. At constant post separation and passage width, the occupation number displays a monotonic decrease with the increasing geometry ratio dc/wp or volume fraction of posts, while a maximum is observed at constant post diameter. The latter finding is attributed to a relaxed conformation of the chains at small dc/wp ratio, which results from a combination of wide interstitial volumes and wide passage apertures. This maximum is approximately positioned at the same dc/wp value for both flexible and semiflexible chains. The chain expansion from a single interstitial volume into more interstitial volumes also starts at the same value of dc/wp ratio for both chains. The dependence of the axial chain extension on the dc/wp ratio turns out to be controlled by the diameter of the interstitial space and by the number of monomers in the individual interstitial volumes. If these two factors act in the same way on the axial extension of chain fragments in interstitial volumes the monotonic increase of the axial chain extension with the dc/wp in the nanopost arrays is observed. At constant wp, however, these two factors act in opposite way and the axial chain extension plotted against the dc/wp ratio exhibits a maximum. In the case of constant post diameter, the characteristic hump in the single chain structure factor whose position correlates with the post separation is found only in the structure factor of the flexible chain confined in the nanopost array of certain value of Sp. The structure factor of the flexible chain contains more information on the monomer organization and mutual correlations than the structure factor of the semiflexible chain. The stiffer chain confined in the nanopost array is composed of low number of statistical segments important for the presence of respective hierarchical regimes in the structure factor.

Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts

The structural properties of a flexible and semiflexible circular chain confined in an array of parallel nanoposts with a square lattice cross-sectional projection were studied using coarse-grained molecular dynamics simulations. To address the effect of the circular topology, a comparison with linear analogs was also carried out. In the interpretation of the chain structural properties, the geometry of the post array is considered as a combination of a channel approximating the interstitial volume with the diameter dc and a slit approximating the passage aperture with the width wp. The number of interstitial volumes occupied by a chain monotonically increases with the decreasing ratio dc/wp regardless of the way the geometry of the post array is varied. However, depending on how the array geometry is modified, the chain span along the posts displays a monotonic (constant post separation) or a non-monotonic behavior (constant passage width) when plotted as a function of the post diameter. In the case of monotonic trend, the width of interstitial spaces increases with the increasing chain occupation number, while, in the case of non-monotonic trend, the width of interstitial spaces decreases with the increasing chain occupation number. In comparison with linear topology, for circular topology, the stiffness affects more significantly the relative chain extension along the posts and less significantly the occupation number. The geometrical parameters of the post arrays are stored in the single-chain structure factors. The characteristic humps are recognized in the structure factor which ensue from the local increase in the density of segments in the circular chains presented in an interstitial volume or from the correlation of parallel chain fragments separated by a row of posts. Although the orientation correlations provide qualitative information about the chain topology and the character of confinement within a single interstitial volume, information about the array periodicity is missing.

Self-Assembly of a [2]Pseudorotaxane by an Inchworm-Motion Mechanism

The threading of biomolecules through pores or channels in membranes is important to validate the physiological activities of cells. To aid understanding of the controlling factors required for the translocation in space with confined size and distorted conformation, it is desirable to identify experimental systems with minimized complexity. We demonstrate the mechanism of a linear guest L1 threading into a tris(crown ether) host TC with a combinational distorted cavity to form a triply interlocked [2]pseudorotaxane 3in-[L1⊂TC]. An inchworm-motion mechanism is proposed for the process. For the forward-threading steps that lead to the formation of higher-order interlocked species, guest L1 must adopt a bent conformation to find the next crown ether cavity. Two simplified models are applied to investigate the self-assembly dynamic of 3in-[L1⊂TC]. Kinetic NMR spectroscopic and molecular dynamics (MD) studies show that formation of the singly penetrated species is fast, whereas formation of the doubly and triply threaded species is several orders of magnitude slower. During threading the freedom of both the guest L1 and host TC gradually decrease due to their interactions. This results in a significant entropy effect for the threading dynamic, which is also observed for the threading of a biomolecular chain through a channel.

Persistence length of DNA molecules confined in nanochannels

The influence of confinement on the persistence length of dsDNA molecules under a high ionic strength environment was explored by coarse-grained Monte Carlo simulations in channels of different profiles. It was found that under confinement three definitions of the persistence length of DNA molecules were not equivalent and represented different properties. In case of the global quantities, the projection and the WLC persistence lengths, the apparent values up to several hundred nanometres are observed for DNA confined in narrow channels. The orientational correlation function cos theta(s) of confined DNA shows a complex pattern, distinctive for semiflexible polymers. At weak and moderate confinements the function cos theta(s) suggests an unexpected increase in the apparent DNA flexibility. The orientational persistence length computed from the initial slope of the function cos theta(s) mirrors only short-scale correlations and gives the value close to the intrinsic persistence length of DNA. The simulation data of direct relevance to experimental studies of DNA in microfluidic devices are compared with analytical theories for stiff chains.

Energy-driven asymmetric partitioning of a semiflexible polymer between interconnected cavities

The distribution of a semiflexible chain in the volume of two interconnected spherical cavities of equal size has been investigated by using Monte Carlo simulations. The chain possessed an extension exceeding that of the cavity, leading to large probabilities of translocated states despite the entropic penalty of passing the narrow passage. Furthermore, an asymmetric state with unequal subchain lengths in the two cavities was more favorable than the symmetric state. The preference for the asymmetric state is driven by the bending energy. Basically, in the symmetric state both subchains are forced to be bent, whereas in the asymmetric case only one of the subchains must bend, leading to an overall smaller bending penalty and overall smaller free energy of the asymmetric state. These results are in contrast to the entropy-controlled partitioning of polymers into confinement and the symmetric translocation state appearing for flexible polymers.

Polymer translocation through a cylindrical channel

A formalism of polymer translocation through a cylindrical channel of finite diameter and length between two spherical compartments is developed. Unlike previous simplified systems, the finite diameter of the channel allows the number of polymer segments inside the channel to be adjusted during translocation according to the free energy of possible conformations. The translocation process of a Gaussian chain without excluded volume and hydrodynamic interactions is studied using exact formulas of confinement free energy under this formalism. The free energy landscape for the translocation process, the distribution of the translocation time, and the average translocation time are presented. The complex dependencies of the average translocation time on the length and diameter of the channel, the sizes of the donor and receptor compartments, and the chain length are illustrated.