title: Effect of nanochannel geometry on DNA structure in the presence of macromolecular crowding agent.
abstract: We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and allow us to develop a deeper understanding of the key physics at play in these systems. It is proposed that the occupancy of free volume next to the channel wall by crowders causes an effective reduction in confining dimensions of the channel that initially swells DNA in nanoconfinement.
authors: Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors: Jeremy J
authors: JJ
authors: Jones
authors: Johan R C
authors: JR
authors: van der Maarel
authors: Patrick S
authors: PS
authors: Doyle
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D046911:Macromolecular Substances / Q000737:chemistry*; D008422:Materials Testing; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure*; D010316:Particle Size
chemical_list: D046911:Macromolecular Substances; D004247:DNA