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Stained DNA Dot Detection (SD3) : An automated tool for quantifying fluorescent features along single stretched DNA molecules

Aning, Obed A. ; Dvirnas, Albertas LU ; Nyblom, My ; Krog, Jens LU ; Carlson, Johanna ; Johansson, Pegah ; Ambjörnsson, Tobias LU and Westerlund, Fredrik (2025) In DNA Repair 149.
Abstract

The main information in DNA is its four-letter sequence that builds up the genetic information and that is traditionally read using sequencing methodologies. DNA can, however, also carry other important information, such as epigenetic marks and DNA damage. This information has recently been visualized along single DNA molecules using fluorescent labels. Quantifying fluorescent labels along DNA is done by counting the number of “dots” per length of each DNA molecule on DNA stretched on a glass surface. So far, a major challenge has been the lack of standardized data analysis tools. Focusing on DNA damage, we here present a Matlab-based automated software, Stained DNA Dot Detection (SD3), which uses a robust method for finding... (More)

The main information in DNA is its four-letter sequence that builds up the genetic information and that is traditionally read using sequencing methodologies. DNA can, however, also carry other important information, such as epigenetic marks and DNA damage. This information has recently been visualized along single DNA molecules using fluorescent labels. Quantifying fluorescent labels along DNA is done by counting the number of “dots” per length of each DNA molecule on DNA stretched on a glass surface. So far, a major challenge has been the lack of standardized data analysis tools. Focusing on DNA damage, we here present a Matlab-based automated software, Stained DNA Dot Detection (SD3), which uses a robust method for finding DNA molecules and estimating the number of dots along each molecule. We have validated SD3 by comparing the outcome to manual analysis using DNA extracted from cells exposed to H2O2 as a model system. Our results show that SD3 achieves high accuracy and reduced analysis time relative to manual counting. SD3 allows the user to define specific parameters regarding the DNA molecule and the location of dots to include during analysis via a user-friendly interface. We foresee that our open-source software can have broad use in the analysis of single DNA molecules and their modifications in research and in diagnostics.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Automated image analysis, DNA analysis, DNA damage, Fluorescence Microscopy, Fluorescent label localization, Single molecule analysis
in
DNA Repair
volume
149
article number
103836
publisher
Elsevier
external identifiers
  • scopus:105003586885
  • pmid:40300455
ISSN
1568-7864
DOI
10.1016/j.dnarep.2025.103836
language
English
LU publication?
yes
additional info
Publisher Copyright: © 2025 The Authors
id
66ea05ca-db5e-4436-b2a9-842c2c621cc3
date added to LUP
2025-08-05 15:09:59
date last changed
2025-08-05 15:10:42
@article{66ea05ca-db5e-4436-b2a9-842c2c621cc3,
  abstract     = {{<p>The main information in DNA is its four-letter sequence that builds up the genetic information and that is traditionally read using sequencing methodologies. DNA can, however, also carry other important information, such as epigenetic marks and DNA damage. This information has recently been visualized along single DNA molecules using fluorescent labels. Quantifying fluorescent labels along DNA is done by counting the number of “dots” per length of each DNA molecule on DNA stretched on a glass surface. So far, a major challenge has been the lack of standardized data analysis tools. Focusing on DNA damage, we here present a Matlab-based automated software, Stained DNA Dot Detection (SD<sup>3</sup>), which uses a robust method for finding DNA molecules and estimating the number of dots along each molecule. We have validated SD<sup>3</sup> by comparing the outcome to manual analysis using DNA extracted from cells exposed to H<sub>2</sub>O<sub>2</sub> as a model system. Our results show that SD<sup>3</sup> achieves high accuracy and reduced analysis time relative to manual counting. SD<sup>3</sup> allows the user to define specific parameters regarding the DNA molecule and the location of dots to include during analysis via a user-friendly interface. We foresee that our open-source software can have broad use in the analysis of single DNA molecules and their modifications in research and in diagnostics.</p>}},
  author       = {{Aning, Obed A. and Dvirnas, Albertas and Nyblom, My and Krog, Jens and Carlson, Johanna and Johansson, Pegah and Ambjörnsson, Tobias and Westerlund, Fredrik}},
  issn         = {{1568-7864}},
  keywords     = {{Automated image analysis; DNA analysis; DNA damage; Fluorescence Microscopy; Fluorescent label localization; Single molecule analysis}},
  language     = {{eng}},
  publisher    = {{Elsevier}},
  series       = {{DNA Repair}},
  title        = {{Stained DNA Dot Detection (SD<sup>3</sup>) : An automated tool for quantifying fluorescent features along single stretched DNA molecules}},
  url          = {{http://dx.doi.org/10.1016/j.dnarep.2025.103836}},
  doi          = {{10.1016/j.dnarep.2025.103836}},
  volume       = {{149}},
  year         = {{2025}},
}