Spontaneous Translocation of Single-Stranded DNA in Graphene-MoS Heterostructure Nanopores: Shape Effect.

The appropriate translocation speed of a single-stranded DNA (ssDNA) through a solid-state nanopore is crucial for DNA sequencing technologies. By studying the geometry effect of graphene-MoS hetero-nanopores with molecular dynamics simulations, we have found that the shape of these nanopores (circular, square, or triangular, with similar size) may have a significant effect on the spontaneous translocation of ssDNA, with the triangular nanopore showing the slowest translocation and the circular one the fastest. Further analyses reveal that such differences in the spontaneous ssDNA translocation arise from different electrostatic attractions between the positively charged Mo atoms exposed in the pore and the negatively charged phosphate groups (PO) in nucleotides; the "sharpness" and the total number of the exposed Mo atoms of the nanopores are responsible for different electrostatic attractions between ssDNA and the nanopore.

Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability.

Mussels can strongly adhere to hydrophilic minerals in sea habitats by secreting adhesive proteins. The adhesion ability of these proteins is often attributed to the presence of Dopa derived from posttranslational modification of Tyr, whereas the contribution of structural feature is overlooked. It remains largely unknown how adhesive proteins overcome the surface-bound water layer to establish underwater adhesion.

Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg Ion Bound at the Double Mg-Clamp Structure.

It has been known that the binding of two Mg ions to the phosphate groups of RNA is essential for enhancing the stability of a three-way junction oligomeric prohead RNA (3WJ-pRNA). Here, we investigate the coupling between binding of two Mg ions and the stability of the complex structure by calculating the rupture force of 3WJ-pRNA using steered molecular dynamics simulations. Our simulations showed that the mechanical stability of the pRNA structure is largely retained with a single Mg ion bound.