Topological differences between chiral DNA knots in confinement

Topological organization is an essential feature of bio-macromolecules affecting their properties, for instance unique protein folding enables proper function of molecular machines, or higher-order organization of DNA enables storage and active usage of genetic information in dense environment inside cell core. Backbone of DNA molecule composed of D-deoxyribose (or D-ribose in RNA) introduces asymmetry leading in complex structure with chiral features at all levels of structural organization from right-handed α-helix in secondary structure, through nucleosome units wrapped around histones, knots and catenanes, up to plectonemes and supercoils. In general, we know that chirality plays an important role in biological systems, yet there are still mysteries to uncover. Abundance of certain form of chiral knots was experimentally discovered [1] by 2D-gel electrophoresis, where the structure of knot was altered by supercoiling. The interplay between chirality of knot and chirality of supercoiling induces symmetry breaking and enhances differences between enantiomers. We would like to apply the same principle with suitable confinement, which could be used for separation of chiral entanglements without altering their structure. In our study, we put various types of knots (chiral, achiral, torus, twist, etc.) in three types of confinement (cylinder, torus, helix) and we investigate structural and dynamical properties of the knots. For our study, we use molecular dynamics simulation, which enables detailed investigation of one molecule system with unified size and pre-defined topology. Progress in chemical synthesis enables tailoring molecules with given geometrical properties. Therefore, experimental application of our system could be conducted for instance by self-assembled chiral nanotubes [2].