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:
https://lup.lub.lu.se/record/7969174
- author
- 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
- organization
- publishing date
- 2015
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Biomicrofluidics
- volume
- 9
- issue
- 4
- article number
- 044114
- publisher
- American Institute of Physics (AIP)
- external identifiers
-
- wos:000360311900016
- pmid:26392826
- scopus:84938878991
- pmid:26392826
- 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
- 2016-04-01 14:17:14
- date last changed
- 2024-02-08 14:07:02
@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.}},
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 (AIP)}},
series = {{Biomicrofluidics}},
title = {{Visualizing the entire DNA from a chromosome in a single frame}},
url = {{http://dx.doi.org/10.1063/1.4923262}},
doi = {{10.1063/1.4923262}},
volume = {{9}},
year = {{2015}},
}