Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1129088
- author
- Gunnarsson, Gudmundur H ; Thormar, Hans G ; Gudmundsson, Bjarki ; Åkesson, Lina LU and Jonsson, Jon J
- publishing date
- 2004
- 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
- pmid:14762200
- 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
- 2016-04-01 12:36:43
- date last changed
- 2022-01-27 07:28:23
@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}},
doi = {{10.1093/nar/gnh018}},
volume = {{32}},
year = {{2004}},
}