title: Revisiting blob theory for DNA diffusivity in slitlike confinement.
abstract: Blob theory has been widely applied to describe polymer conformations and dynamics in nanoconfinement. In slit confinement, blob theory predicts a scaling exponent of 2/3 for polymer diffusivity as a function of slit height, yet a large body of experimental studies using DNA produce a scaling exponent significantly less than 2/3. In this work, we develop a theory that predicts that this discrepancy occurs because the segment correlation function for a semiflexible chain such as DNA does not follow the Flory exponent for length scales smaller than the persistence length. We show that these short length scale effects contribute significantly to the scaling for the DNA diffusivity, but do not appreciably affect the scalings for static properties. Our theory is fully supported by Monte Carlo simulations, quantitative agreement with DNA experiments, and the results reconcile this outstanding problem for confined polymers.
authors.affiliation: BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543, Singapore.
authors.forename: Liang
authors.initials: L
authors.lastname: Dai
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Tree
authors.forename: Johan R C
authors.initials: JR
authors.lastname: van der Maarel
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Dorfman
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Doyle
mesh_terms: D020029:Base Pairing; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D008956:Models, Chemical; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D004247:DNA