Design of Histone-Mimic Nanoparticles for DNA and RNA Compaction using Molecular Modeling

Abstract

The design of nanoparticles that can induce specific structural transitions in nucleic acids is important for nanotechnology applications including gene delivery and nanoelectronics. It is known that in biological systems, the binding of cationic proteins induces structural changes in DNA or RNA, which can affect gene expression or cause the compaction of DNA into chromatin. The anionic backbone of the nucleic acids DNA and RNA allow for non-specific electrostatic interactions with cationic proteins, nanoparticles, or dendrimers. The interaction of nucleic acids and nanoparticles may be tuned through changes in nanoparticle size, charge, polarity, or shape. However, the factors that affect structural transitions are not fully understood. We performed atomistic molecular dynamics simulations of the binding of nucleic acids to monolayer-protected gold nanoparticles to elucidate structural changes that take place for nanoparticles and DNA upon binding. Results from these simulations were analyzed to determine modes of DNA and RNA bending with nanoparticles. Our simulations show that highly charged nanoparticles cause DNA to bend with little damage to the helix structure, similar to DNA in the nucleosome. Nanoparticle shape as well as charge is shown to affect the wrapping of nucleic acids with the nanoparticle. Low salt concentrations and high nanoparticle charge cause greater disruptions to DNA structure. We find that the roll parameter is the most important base-pair parameter for DNA bending. Requirements for bending differed significantly between DNA and dsRNA. The degree of DNA bending is controlled by the charge of the NPs, but ligand flexibility played a more significant role in dsRNA bending. We have shown that functionalized gold NPs can be designed to wrap and compact both RNA an DNAs with fine control of binding strength through NP charge and ligand chemistry.