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Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples

Gunnarsson, Gudmundur H; Thormar, Hans G; Gudmundsson, Bjarki; Åkesson, Lina LU and Jonsson, Jon J (2004) In Nucleic Acids Research 32(2). p.23-23
Abstract
DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from those perfectly matched; (ii) simultaneous, diagnostic, mismatch scanning of multiple fragments; (iii) isolation of damaged DNA fragments from undamaged fragments; and (iv) estimation of reannealing efficiency of complex DNA samples. We developed a two-dimensional conformation-dependent electrophoresis (2D-CDE) method for separating DNA fragments based on length and conformation in the first dimension and only on length in... (More)
DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from those perfectly matched; (ii) simultaneous, diagnostic, mismatch scanning of multiple fragments; (iii) isolation of damaged DNA fragments from undamaged fragments; and (iv) estimation of reannealing efficiency of complex DNA samples. We developed a two-dimensional conformation-dependent electrophoresis (2D-CDE) method for separating DNA fragments based on length and conformation in the first dimension and only on length in the second dimension. Differences in migration velocity due to conformation were minimized during second dimension electrophoresis by introducing an intercalator. To test the method, we constructed 298 bp DNA fragments containing cytosine bulges ranging from 1 to 5 nt. Bulge-containing DNA fragments had reduced migration velocity in the first dimension due to altered conformation. After 2D-CDE, bulge-containing DNA fragments had migrated in front of an arc comprising heterogeneous fragments with regular conformation. This simple and robust method could be used in both analytical and preparative applications involving complex DNA samples. (Less)
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author
publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
32
issue
2
pages
23 - 23
publisher
Oxford University Press
external identifiers
  • pmid:14762200
  • scopus:17144451875
ISSN
1362-4962
DOI
10.1093/nar/gnh018
language
English
LU publication?
no
id
ae618fea-8f53-4504-9079-f7004eacb070 (old id 1129088)
date added to LUP
2008-06-13 14:50:56
date last changed
2017-01-01 05:17:55
@article{ae618fea-8f53-4504-9079-f7004eacb070,
  abstract     = {DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from those perfectly matched; (ii) simultaneous, diagnostic, mismatch scanning of multiple fragments; (iii) isolation of damaged DNA fragments from undamaged fragments; and (iv) estimation of reannealing efficiency of complex DNA samples. We developed a two-dimensional conformation-dependent electrophoresis (2D-CDE) method for separating DNA fragments based on length and conformation in the first dimension and only on length in the second dimension. Differences in migration velocity due to conformation were minimized during second dimension electrophoresis by introducing an intercalator. To test the method, we constructed 298 bp DNA fragments containing cytosine bulges ranging from 1 to 5 nt. Bulge-containing DNA fragments had reduced migration velocity in the first dimension due to altered conformation. After 2D-CDE, bulge-containing DNA fragments had migrated in front of an arc comprising heterogeneous fragments with regular conformation. This simple and robust method could be used in both analytical and preparative applications involving complex DNA samples.},
  author       = {Gunnarsson, Gudmundur H and Thormar, Hans G and Gudmundsson, Bjarki and Åkesson, Lina and Jonsson, Jon J},
  issn         = {1362-4962},
  language     = {eng},
  number       = {2},
  pages        = {23--23},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples},
  url          = {http://dx.doi.org/10.1093/nar/gnh018},
  volume       = {32},
  year         = {2004},
}