Nanochannel confinement: DNA stretch approaching full contour length

• Published in: Lab on a chip 2011-05, Vol.11 (10), p.1721-1729
• Main Authors: Kim, Yoori, Kim, Ki Seok, Kounovsky, Kristy L, Chang, Rakwoo, Jung, Gun Young, dePablo, Juan J, Jo, Kyubong, Schwartz, David C
• Format: Article
• Language: English
• Subjects: Benzoxazoles - chemistry; Dimethylpolysiloxanes - chemistry; DNA - chemistry; Monte Carlo Method; Nanostructures - chemistry; Osmolar Concentration; Quinolinium Compounds - chemistry
• ISSN: 1473-0189; 1473-0197; 1473-0189
• DOI: 10.1039/c0lc00680g

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.