Single-molecule denaturation mapping of DNA in nanofluidic channels
Reisner, Walter ; Larsen, Niels B. ; Silahtaroglu, Asli ; Kristensen, Anders ; Tommerup, Niels ; Tegenfeldt, Jonas LU
and Flyvbjerg, Henrik
(2010)
In Proceedings of the National Academy of Sciences
107(30).
p.13294-13299
- Abstract
- Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the... (More)
- Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1672604
- author
- Reisner, Walter
; Larsen, Niels B.
; Silahtaroglu, Asli
; Kristensen, Anders
; Tommerup, Niels
; Tegenfeldt, Jonas
LU
and Flyvbjerg, Henrik
- organization
- publishing date
- 2010
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- DNA optical mapping, DNA barcoding, DNA denaturation, nanochannel
- in
- Proceedings of the National Academy of Sciences
- volume
- 107
- issue
- 30
- pages
- 13294 - 13299
- publisher
- National Academy of Sciences
- external identifiers
-
- wos:000280602800022
- scopus:77955829945
- pmid:20616076
- ISSN
- 1091-6490
- DOI
- 10.1073/pnas.1007081107
- language
- English
- LU publication?
- yes
- id
- 8234947e-c081-4209-854f-abccf8287343 (old id 1672604)
- date added to LUP
- 2016-04-01 10:51:18
- date last changed
- 2023-11-10 06:41:53
@article{8234947e-c081-4209-854f-abccf8287343,
abstract = {{Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.}},
author = {{Reisner, Walter and Larsen, Niels B. and Silahtaroglu, Asli and Kristensen, Anders and Tommerup, Niels and Tegenfeldt, Jonas and Flyvbjerg, Henrik}},
issn = {{1091-6490}},
keywords = {{DNA optical mapping; DNA barcoding; DNA denaturation; nanochannel}},
language = {{eng}},
number = {{30}},
pages = {{13294--13299}},
publisher = {{National Academy of Sciences}},
series = {{Proceedings of the National Academy of Sciences}},
title = {{Single-molecule denaturation mapping of DNA in nanofluidic channels}},
url = {{http://dx.doi.org/10.1073/pnas.1007081107}},
doi = {{10.1073/pnas.1007081107}},
volume = {{107}},
year = {{2010}},
}