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Nanochannel confinement: DNA stretch approaching full contour length

2011; Royal Society of Chemistry; Volume: 11; Issue: 10 Linguagem: Inglês

10.1039/c0lc00680g

1473-0197

Yoori Kim, Ki Seok Kim, Kristy L. Kounovsky, Rakwoo Chang, Gun Young Jung, Juan J. dePablo, Kyubong Jo, David C. Schwartz,

Advanced biosensing and bioanalysis techniques

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.