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Enzyme-free optical DNA mapping of the human genome using competitive binding

Müller, Vilhelm; Dvirnas, Albertas LU ; Andersson, John; Singh, Vandana; Kk, Sriram; Johansson, Pegah; Ebenstein, Yuval; Ambjörnsson, Tobias LU and Westerlund, Fredrik (2019) In Nucleic Acids Research 47(15).
Abstract

Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate... (More)

Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
47
issue
15
publisher
Oxford University Press
external identifiers
  • scopus:85072057464
ISSN
1362-4962
DOI
10.1093/nar/gkz489
language
English
LU publication?
yes
id
72a7ff44-341f-4734-ab4f-17c28e9e5c4f
date added to LUP
2019-09-16 14:51:21
date last changed
2019-10-15 07:16:29
@article{72a7ff44-341f-4734-ab4f-17c28e9e5c4f,
  abstract     = {<p>Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.</p>},
  articleno    = {e89},
  author       = {Müller, Vilhelm and Dvirnas, Albertas and Andersson, John and Singh, Vandana and Kk, Sriram and Johansson, Pegah and Ebenstein, Yuval and Ambjörnsson, Tobias and Westerlund, Fredrik},
  issn         = {1362-4962},
  language     = {eng},
  month        = {09},
  number       = {15},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Enzyme-free optical DNA mapping of the human genome using competitive binding},
  url          = {http://dx.doi.org/10.1093/nar/gkz489},
  volume       = {47},
  year         = {2019},
}