Abstract
Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.
Helix structure of dextran sulphate sodium in an aqueous environment. Sodium cations are positioned in pairs between the two sulphate ester groups on each glucose ring. DSS structure are displayed as tubes. Solvent water molecules are displayed as lines for clarity. Grey: carbon, red: oxygen, white: hydrogen connection, yellow: sulfur and blue: sodium cation. [Display omitted]
•A three-dimensional helical molecular structure of dextran sulphate sodium (DSS) was determined via molecular modelling.•A size-limited specific interaction is expected during the translocation of DSS via model α-hemolysin nano-pores.