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  Probing hairpin structures of small DNAs by nondenaturing polyacrylamide gel electrophoresis.

Baumann, U., Frank, R., & Blöcker, H. (1989). Probing hairpin structures of small DNAs by nondenaturing polyacrylamide gel electrophoresis. Analytical Biochemistry, 1813(1), 152-158. doi:10.1016/0003-2697(89)90183-8.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-279F-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-27A3-2
Genre: Journal Article

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Baumann, U.1, Author              
Frank, R., Author
Blöcker, H., Author
Affiliations:
1Research Group of Molecular Organized Systems, MPI for biophysical chemistry, Max Planck Society, ou_578548              

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 Abstract: The influence of temperature on the electrophoretic mobility of small DNAs, capable of forming hairpin structures, is investigated under nondenaturing conditions. Three series of hairpin-forming DNAs containing different numbers of thymidine, deoxyadenosine, and deoxyguanosine residues in their loop, and an identical sequence in the helical region, are analyzed. All show enhanced electrophoretic mobility if they adopt the hairpin conformation. The same quantitative relationship between hairpin formation and increase in electrophoretic mobility is observed for all of the three series. The constancy of this increase suggests a dependence of electrophoretic acceleration on the length of the helical region. A possible application of nondenaturing electrophoresis is monitoring the hairpin/coil transition. Another possible application is the detection of dimers formed by partially self-complementary sequences. This dimer formation is detected for completely complementary DNAs, whereas sequences which might form imperfect double helices, especially those with three bulged-out nucleotides, prefer hairpin formation. The possible applications are experimentally approached and discussed.

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Language(s): eng - English
 Dates: 1989-11-15
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1016/0003-2697(89)90183-8
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Title: Analytical Biochemistry
Source Genre: Journal
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Pages: - Volume / Issue: 1813 (1) Sequence Number: - Start / End Page: 152 - 158 Identifier: -