Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study.

In Förster resonance energy transfer (FRET) experiments, extracting accurate structural information about macromolecules depends on knowing the positions and orientations of donor and acceptor fluorophores. Several approaches have been employed to reduce uncertainties in quantitative FRET distance measurements. Fluorophore-position distributions can be estimated by surface accessibility (SA) calculations, which compute the region of space explored by the fluorophore within a static macromolecular structure. However, SA models generally do not take fluorophore shape, dye transition-moment orientation, or dye-specific chemical interactions into account. We present a detailed molecular-dynamics (MD) treatment of fluorophore dynamics for an ATTO donor/acceptor dye pair and specifically consider as case studies dye-labeled protein-DNA intermediates in Cre site-specific recombination. We carried out MD simulations in both an aqueous solution and glycerol/water mixtures to assess the effects of experimental solvent systems on dye dynamics. Our results unequivocally show that MD simulations capture solvent effects and dye-dye interactions that can dramatically affect energy transfer efficiency. We also show that results from SA models and MD simulations strongly diverge in cases where donor and acceptor fluorophores are in close proximity. Although atomistic simulations are computationally more expensive than SA models, explicit MD studies are likely to give more realistic results in both homogeneous and mixed solvents. Our study underscores the model-dependent nature of FRET analyses, but also provides a starting point to develop more realistic in silico approaches for obtaining experimental ensemble and single-molecule FRET data.

A mean field approach for computing solid-liquid surface tension for nanoscale interfaces.

The physical properties of a liquid in contact with a solid are largely determined by the solid-liquid surface tension. This is especially true for nanoscale systems with high surface area to volume ratios. While experimental techniques can only measure surface tension indirectly for nanoscale systems, computer simulations offer the possibility of a direct evaluation of solid-liquid surface tension although reliable methods are still under development. Here we show that using a mean field approach yields great physical insight into the calculation of surface tension and into the precise relationship between surface tension and excess solvation free energy per unit surface area for nanoscale interfaces. Previous simulation studies of nanoscale interfaces measure either excess solvation free energy or surface tension, but these two quantities are only equal for macroscopic interfaces. We model the solid as a continuum of uniform density in analogy to Hamaker's treatment of colloidal particles. As a result, the Hamiltonian of the system is imbued with parametric dependence on the size of the solid object through the integration limits for the solid-liquid interaction energy. Since the solid-liquid surface area is a function of the size of the solid, and the surface tension is the derivative of the system free energy with respect to this surface area, we obtain a simple expression for the surface tension of an interface of arbitrary shape. We illustrate our method by modeling a thin nanoribbon and a solid spherical nanoparticle. Although the calculation of solid-liquid surface tension is a demanding task, the method presented herein offers new insight into the problem, and may prove useful in opening new avenues of investigation.

Natural Carriers for siRNA Delivery.

This review is based on carriers of natural origin such as polysaccharides, proteins, and cell derived entities which have been used for delivery of siRNA. To realize the therapeutic potential of a delivery system, the role of the carrier is of utmost importance. Historical aspects of viral vectors, the first carriers of genes are briefly outlined. Chitosan, one of the extensively experimented carriers, alginates and other polysaccharides have shown success in siRNA delivery. Peptides of natural origin and mimics thereof have emerged as another versatile carrier. Exosomes and mini cells of cellular origin are the newest entrants to the area of siRNA delivery and probably the closest one can get to a natural carrier. In many of the carriers, modifications have provided better efficiency in delivery. The salient features of the carriers and their advantages and disadvantages are also reviewed.