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Bacteriophage strain typing by rapid single molecule analysis.

Grunwald, Assaf; Dahan, Moran; Giesbertz, Anna; Nilsson, Adam LU ; Nyberg, Lena K; Weinhold, Elmar; Ambjörnsson, Tobias LU ; Westerlund, Fredrik and Ebenstein, Yuval (2015) In Nucleic Acids Research 43(18). p.117-117
Abstract
Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the... (More)
Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of λ and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems. (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
Nucleic Acids Research
volume
43
issue
18
pages
117 - 117
publisher
Oxford University Press
external identifiers
  • pmid:26019180
  • wos:000366406500003
  • scopus:84983802912
ISSN
1362-4962
DOI
10.1093/nar/gkv563
language
English
LU publication?
yes
id
4dc9c2a9-6488-4464-abd3-0aa02cdc253b (old id 5441960)
date added to LUP
2015-06-17 15:37:51
date last changed
2017-10-01 03:01:18
@article{4dc9c2a9-6488-4464-abd3-0aa02cdc253b,
  abstract     = {Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of λ and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.},
  author       = {Grunwald, Assaf and Dahan, Moran and Giesbertz, Anna and Nilsson, Adam and Nyberg, Lena K and Weinhold, Elmar and Ambjörnsson, Tobias and Westerlund, Fredrik and Ebenstein, Yuval},
  issn         = {1362-4962},
  language     = {eng},
  number       = {18},
  pages        = {117--117},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Bacteriophage strain typing by rapid single molecule analysis.},
  url          = {http://dx.doi.org/10.1093/nar/gkv563},
  volume       = {43},
  year         = {2015},
}