title: Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics.
abstract: The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.
authors.affiliation: Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States.
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Nash
authors.affiliation: Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Singh
authors.affiliation: Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States.
authors.forename: Nan K
authors.initials: NK
authors.lastname: Li
authors.affiliation: Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States.
authors.forename: Yaroslava G
authors.initials: YG
authors.lastname: Yingling
mesh_terms: D006046:Gold / Q000737:chemistry; D006657:Histones / Q000737:chemistry*; D053768:Metal Nanoparticles / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure
chemical_list: D006657:Histones; D009696:Nucleic Acids; D006046:Gold
keywords: DNA compaction; RNA compaction; gold nanoparticles; molecular dynamics simulations; nanoparticle binding; nucleosome