title: Mixed confinement regimes during equilibrium confinement spectroscopy of DNA.
abstract: We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the "mixing" of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter.
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors.forename: Damini
authors.initials: D
authors.lastname: Gupta
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors.forename: Julian
authors.initials: J
authors.lastname: Sheats
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors.forename: Abhiram
authors.initials: A
authors.lastname: Muralidhar
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Miller
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors.forename: Derek E
authors.initials: DE
authors.lastname: Huang
authors.affiliation: Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
authors.forename: Sara
authors.initials: S
authors.lastname: Mahshid
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Dorfman
authors.affiliation: Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
authors.forename: Walter
authors.initials: W
authors.lastname: Reisner
mesh_terms: D004247:DNA / Q000737:chemistry / Q000648:ultrastructure*; D007364:Intercalating Agents; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D013057:Spectrum Analysis
chemical_list: D007364:Intercalating Agents; D004247:DNA