title: Amplified stretch of bottlebrush-coated DNA in nanofluidic channels.
abstract: The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.
authors.affiliation: Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Ce
authors.initials: C
authors.lastname: Zhang
authors.forename: Armando
authors.initials: A
authors.lastname: Hernandez-Garcia
authors.forename: Kai
authors.initials: K
authors.lastname: Jiang
authors.forename: Zongying
authors.initials: Z
authors.lastname: Gong
authors.forename: Durgarao
authors.initials: D
authors.lastname: Guttula
authors.forename: Siow Yee
authors.initials: SY
authors.lastname: Ng
authors.forename: Piravi P
authors.initials: PP
authors.lastname: Malar
authors.forename: Jeroen A
authors.initials: JA
authors.lastname: van Kan
authors.forename: Liang
authors.initials: L
authors.lastname: Dai
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Doyle
authors.forename: Renko de
authors.initials: Rd
authors.lastname: Vries
authors.forename: Johan R C
authors.initials: JR
authors.lastname: van der Maarel
mesh_terms: D002874:Chromosome Mapping; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation; D018625:Microscopy, Atomic Force; D008856:Microscopy, Fluorescence; D009010:Monte Carlo Method; D049329:Nanostructures / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*
chemical_list: D010455:Peptides; D004247:DNA