Nanochannel confinement: DNA stretch approaching full contour length

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

Research output: Contribution to journalArticle

108 Citations (Scopus)

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 m ± 1.1 m for YOYO-1 stained λ DNA (21.8 m 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.

Original languageEnglish (US)
Pages (from-to)1721-1729
Number of pages9
JournalLab on a Chip
Volume11
Issue number10
DOIs
StatePublished - May 21 2011

Fingerprint

DNA
Physics
Molecules
Polymers
Nanofluidics
Biota
Ionic strength
Computer Simulation
Osmolar Concentration
Stretching
Genes
Genome
Computer simulation

ASJC Scopus subject areas

  • Bioengineering
  • Biochemistry
  • Chemistry(all)
  • Biomedical Engineering

Cite this

Kim, Y., Kim, K. S., Kounovsky, K. L., Chang, R., Jung, G. Y., Depablo, J. J., ... Schwartz, D. C. (2011). Nanochannel confinement: DNA stretch approaching full contour length. Lab on a Chip, 11(10), 1721-1729. https://doi.org/10.1039/c0lc00680g

Nanochannel confinement : DNA stretch approaching full contour length. / Kim, Yoori; Kim, Ki Seok; Kounovsky, Kristy L.; Chang, Rakwoo; Jung, Gun Young; Depablo, Juan J.; Jo, Kyubong; Schwartz, David C.

In: Lab on a Chip, Vol. 11, No. 10, 21.05.2011, p. 1721-1729.

Research output: Contribution to journalArticle

Kim, Y, Kim, KS, Kounovsky, KL, Chang, R, Jung, GY, Depablo, JJ, Jo, K & Schwartz, DC 2011, 'Nanochannel confinement: DNA stretch approaching full contour length', Lab on a Chip, vol. 11, no. 10, pp. 1721-1729. https://doi.org/10.1039/c0lc00680g
Kim, Yoori ; Kim, Ki Seok ; Kounovsky, Kristy L. ; Chang, Rakwoo ; Jung, Gun Young ; Depablo, Juan J. ; Jo, Kyubong ; Schwartz, David C. / Nanochannel confinement : DNA stretch approaching full contour length. In: Lab on a Chip. 2011 ; Vol. 11, No. 10. pp. 1721-1729.
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