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Issue 10, 2011
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Nanochannel confinement: DNA stretch approaching full contour length

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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.

Graphical abstract: Nanochannel confinement: DNA stretch approaching full contour length

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Publication details

The article was received on 10 Dec 2010, accepted on 25 Feb 2011 and first published on 23 Mar 2011


Article type: Paper
DOI: 10.1039/C0LC00680G
Citation: Lab Chip, 2011,11, 1721-1729
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    Nanochannel confinement: DNA stretch approaching full contour length

    Y. Kim, K. S. Kim, K. L. Kounovsky, R. Chang, G. Y. Jung, J. J. dePablo, K. Jo and D. C. Schwartz, Lab Chip, 2011, 11, 1721
    DOI: 10.1039/C0LC00680G

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