title: Nanochannel confinement: DNA stretch approaching full contour length.
abstract: Fully stretched DNA molecules are becoming a fundamental component of new systems for comprehensive genome analysis. Among a number of approaches for elongating DNA molecules, nanofluidic molecular confinement has received enormous attentions from physical and biological communities for the last several years. Here we demonstrate a well-optimized condition that a DNA molecule can stretch almost to its full contour length: the average stretch is 19.1 µm ± 1.1 µm for YOYO-1 stained λ DNA (21.8 µm contour length) in 250 nm × 400 nm channel, which is the longest stretch value ever reported in any nanochannels or nanoslits. In addition, based on Odijk's polymer physics theory, we interpret our experimental findings as a function of channel dimensions and ionic strengths. Furthermore, we develop a Monte Carlo simulation approach using a primitive model for the rigorous understanding of DNA confinement effects. Collectively, we present a more complete understanding of nanochannel confined DNA stretching via the comparisons to computer simulation results and Odijk's polymer physics theory.
authors: Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea.
authors: Yoori
authors: Y
authors: Kim
authors: Ki Seok
authors: KS
authors: Kim
authors: Kristy L
authors: KL
authors: Kounovsky
authors: Rakwoo
authors: R
authors: Chang
authors: Gun Young
authors: GY
authors: Jung
authors: Juan J
authors: JJ
authors: dePablo
authors: Kyubong
authors: K
authors: Jo
authors: David C
authors: DC
authors: Schwartz
mesh_terms: D001583:Benzoxazoles / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004129:Dimethylpolysiloxanes / Q000737:chemistry; D009010:Monte Carlo Method; D049329:Nanostructures / Q000737:chemistry*; D009994:Osmolar Concentration; D011806:Quinolinium Compounds / Q000737:chemistry
chemical_list: D001583:Benzoxazoles; D004129:Dimethylpolysiloxanes; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; C013830:baysilon; D004247:DNA