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Biomicrofluidics / Volume 5 / Issue 3 / REGULAR ARTICLES

Biomicrofluidics 5, 034106 (2011); http://dx.doi.org/10.1063/1.3613671 (8 pages)

DNA methylation profiling in nanochannels

Shuang Fang Lim, Alena Karpusenko, John J. Sakon, Joseph A. Hook, Tyra A. Lamar, and Robert Riehn

Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA

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(Received 29 April 2011; accepted 24 June 2011; published online 25 July 2011)

We report the profiling of the 5-methyl cytosine distribution within single genomic-sized DNA molecules at a gene-relevant resolution. This method linearizes and stretches DNA molecules by confinement to channels with a dimension of about 250×200nm2. The methylation state is detected using fluorescently labeled methyl-CpG binding domain proteins (MBD), with high signal contrast and low background. DNA barcodes consisting of methylated and non-methylated segments are generated, with both short and long concatemers demonstrating spatially resolved MBD binding. The resolution of the technique is better than 10 kbp, and single-molecule read-lengths exceeding 140 kbp have been achieved.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. MATERIALS AND METHODS
    1. Preparation of essential biological materials
    2. Controls
    3. DNA concatemer formation and staining
    4. Operational procedure of observation
  3. RESULTS AND DISCUSSION
  4. CONCLUSIONS

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KEYWORDS and PACS

Keywords

biochemistry, DNA, genetics, molecular biophysics, proteins

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3613671

PUBLICATION DATA

ISSN

1932-1058 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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Figures (4)

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