Polyelectrolytes confined to spherical cavities

The effects of confining a polyelectrolyte solution containing a polyion and its counterions in spherical cavities of different sizes have been investigated by Monte Carlo simulations using a simple model system. Polyions of three different linear charge densities and counterions of three different valences have been examined. Structure, energy, and free energy properties of all systems have been determined as a function of the sphere radius. In nearly all cases, the free energy of confining the polyelectrolyte solution increases as the sphere radius is decreased. The free energy cost decreases as the linear charge density of the polyion is reduced and as the counterion valence is increased, although for completely different reasons. A strong consistency among the variations of the different structural and thermodynamic results on the linear charge density and counterion valence was found. The study provides information relevant for experimental systems of polyions confined to, e.g., viruses, vesicles, and zeolite cavities. (C) 2002 American Institute of Physics

Exploring PAZ/3′-overhang interaction to improve siRNA specificity: a combined experimental and modeling study

The understanding of the dynamical and mechanistic aspects that lie behind siRNA-based gene regulation is a requisite to boost the performance of siRNA therapeutics. A systematic experimental and computational study on the 3′-overhang structural requirements for the design of more specific and potent siRNA molecules was carried out using nucleotide analogues differing in structural parameters, such as sugar constraint, lack of nucleobase, distance between the phosphodiester backbone and nucleobase, enantioselectivity, and steric hindrance. The results established a set of rules governing the siRNA-mediated silencing, indicating that the thermodynamic stability of the 5′-end is a crucial determinant for antisense-mediated silencing but is not sufficient to avoid sense-mediated silencing. Both theoretical and experimental approaches consistently evidence the existence of a direct connection between the PAZ/3′-overhang binding affinity and siRNA’s potency and specificity. An overall description of the systems is thus achieved by atomistic simulations and free energy calculations that allow us to propose a robust and self-contained procedure for studying the factors implied in PAZ/3′-overhang siRNA interactions. A higher RNAi activity is associated with a moderate-to-strong PAZ/3′-overhang binding. Contrarily, lower binding energies compromise siRNA potency, increase specificity, and favor siRNA downregulation by Ago2-independent mechanisms. This work provides in-depth details for the design of powerful and safe synthetic nucleotide analogues for substitution at the 3′-overhang, enabling some of the intrinsic siRNA disadvantages to be overcome