Complexation of siRNA with dendrimer: A molecular modeling approach

Abstract

This paper reports the structural behavior and thermodynamics of the complexation of siRNA with poly(amidoamine) (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) through fully atomistic molecular dynamics (MD) simulations accompanied by free energy calculations and inherent structure determination. We have also done simulation with one siRNA and two dendrimers (2×G3 or 2×G4) to get the microscopic picture of various binding modes. Our simulation results reveal the formation of stable siRNA−dendrimer complex over nanosecond time scale. With the increase in dendrimer generation, the charge ratio increases and hence the binding energy between siRNA and dendrimer also increases in accordance with available experimental measurements. Calculated radial distribution functions of amines groups of various subgenerations in a given generation of dendrimer and phosphate in backbone of siRNA reveals that one dendrimer of generation 4 shows better binding with siRNA almost wrapping the dendrimer when compared to the binding with lower generation dendrimer like G3. In contrast, two dendrimers of generation 4 show binding without siRNA wrapping the dendrimer because of repulsion between two dendrimers. The counterion distribution around the complex and the water molecules in the hydration shell of siRNA give microscopic picture of the binding dynamics. We see a clear correlation between water, counterions motions and the complexation i.e. the water molecules and counterions which condensed around siRNA are moved away from the siRNA backbone when dendrimer start binding to the siRNA backbone. As siRNA wraps/bind to the dendrimer counterions originally condensed onto siRNA (Na⁺) and dendrimer (Cl^-) get released. We give a quantitative estimate of the entropy of counterions and show that there is gain in entropy due to counterions release during the complexation. Furthermore, the free energy of complexation of 1G3 and 1G4 at two different salt concentrations shows that increase in salt concentration leads to the weakening of the binding affinity of siRNA and dendrimer.