Two-dimensional strandness-dependent electrophoresis: a method to characterize single-stranded DNA, double-stranded DNA, and RNA-DNA hybrids in complex samples
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
MetadataShow full item record
CitationAnal. Biochem. 2006, 350(1):120-7
AbstractWe describe two-dimensional strandness-dependent electrophoresis (2D-SDE) for quantification and length distribution analysis of single-stranded (ss) DNA fragments, double-stranded (ds) DNA fragments, RNA-DNA hybrids, and nicked DNA fragments in complex samples. In the first dimension nucleic acid molecules are separated based on strandness and length in the presence of 7 M urea. After the first-dimension electrophoresis all nucleic acid fragments are heat denatured in the gel. During the second-dimension electrophoresis all nucleic acid fragments are single-stranded and migrate according to length. 2D-SDE takes about 90 min and requires only basic skills and equipment. We show that 2D-SDE has many applications in analyzing complex nucleic acid samples including (1) estimation of renaturation efficiency and kinetics, (2) monitoring cDNA synthesis, (3) detection of nicked DNA fragments, and (4) estimation of quality and in vitro damage of nucleic acid samples. Results from 2D-SDE should be useful to validate techniques such as complex polymerase chain reaction, subtractive hybridization, cDNA synthesis, cDNA normalization, and microarray analysis. 2D-SDE could also be used, e.g., to characterize biological nucleic acid samples. Information obtained with 2D-SDE cannot be readily obtained with other methods. 2D-SDE can be used for preparative isolation of ssDNA fragments, dsDNA fragments, and RNA-DNA hybrids.
DescriptionTo access publisher full text version of this article. Please click on the hyperlink in Additional Links field
- Two-dimensional strandness-dependent electrophoresis.
- Authors: Gunnarsson GH, Gudmundsson B, Thormar HG, Alfredsson A, Jonsson JJ
- Issue date: 2006
- Importance of the efficiency of double-stranded DNA formation in cDNA synthesis for the imprecision of microarray expression analysis.
- Authors: Thormar HG, Gudmundsson B, Eiriksdottir F, Kil S, Gunnarsson GH, Magnusson MK, Hsu JC, Jonsson JJ
- Issue date: 2013 Apr
- Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples.
- Authors: Gunnarsson GH, Thormar HG, Gudmundsson B, Akesson L, Jonsson JJ
- Issue date: 2004 Feb 3
- Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis.
- Authors: Hegedüs E, Kókai E, Kotlyar A, Dombrádi V, Szabó G
- Issue date: 2009 Sep
- Isolation and characterization of DNA-DNA and DNA-RNA.
- Authors: Salzberg S, Levi Z, Aboud M, Goldberger A
- Issue date: 1977 Jan 11