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Visualizing the entire DNA from a chromosome in a single frame

Freitag, C.; Noble, Charleston LU ; Fritzsche, J.; Persson, F.; Reiter-Schad, Michaela LU ; Nilsson, Adam LU ; Graneli, A.; Ambjörnsson, Tobias LU ; Mir, K. U. and Tegenfeldt, Jonas LU (2015) In Biomicrofluidics 9(4).
Abstract
The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field... (More)
The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biomicrofluidics
volume
9
issue
4
publisher
American Institute of Physics
external identifiers
  • wos:000360311900016
  • pmid:26392826
  • scopus:84938878991
ISSN
1932-1058
DOI
10.1063/1.4923262
language
English
LU publication?
yes
id
2465df78-5ac8-4039-a7c3-ec4388391f53 (old id 7969174)
date added to LUP
2015-09-23 07:07:54
date last changed
2017-07-02 04:05:27
@article{2465df78-5ac8-4039-a7c3-ec4388391f53,
  abstract     = {The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.},
  articleno    = {044114},
  author       = {Freitag, C. and Noble, Charleston and Fritzsche, J. and Persson, F. and Reiter-Schad, Michaela and Nilsson, Adam and Graneli, A. and Ambjörnsson, Tobias and Mir, K. U. and Tegenfeldt, Jonas},
  issn         = {1932-1058},
  language     = {eng},
  number       = {4},
  publisher    = {American Institute of Physics},
  series       = {Biomicrofluidics},
  title        = {Visualizing the entire DNA from a chromosome in a single frame},
  url          = {http://dx.doi.org/10.1063/1.4923262},
  volume       = {9},
  year         = {2015},
}