Nanochannel confinement: DNA stretch approaching full contour length |
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Authors: | Kim Yoori Kim Ki Seok Kounovsky Kristy L Chang Rakwoo Jung Gun Young dePablo Juan J Jo Kyubong Schwartz David C |
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Affiliation: | Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea. |
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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. |
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