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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)
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author
organization
publishing date
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 Acad Sciences
external identifiers
  • wos:000280602800022
  • scopus:77955829945
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
2010-09-23 13:42:26
date last changed
2018-06-24 03:28:35
@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},
  keyword      = {DNA optical mapping,DNA barcoding,DNA denaturation,nanochannel},
  language     = {eng},
  number       = {30},
  pages        = {13294--13299},
  publisher    = {National Acad 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},
  volume       = {107},
  year         = {2010},
}