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Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis.

ABSTRACT: Double-stranded (ds), as well as denatured, single-stranded (ss) DNA samples can be analyzed on urea-agarose gels. Here we report that after denaturation by heat in the presence of 8 M urea, the two strands of the same ds DNA fragment of approximately 1-20-kb size migrate differently in 1 M urea containing agarose gels. The two strands are readily distinguished on Southern blots by ss-specific probes. The different migration of the two strands could be attributed to their different, base composition-dependent conformation impinging on the electrophoretic mobility of the ss molecules. This phenomenon can be exploited for the efficient preparation of strand-specific probes and for the separation of the complementary DNA strands for subsequent analysis, offering a new tool for various cell biological research areas.

SUBMITTER: Hegedus E

PROVIDER: S-EPMC2761254 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis.

Hegedüs Eva E Kókai Endre E Kotlyar Alexander A Dombrádi Viktor V Szabó Gábor G

Nucleic acids research 20090623 17

Double-stranded (ds), as well as denatured, single-stranded (ss) DNA samples can be analyzed on urea-agarose gels. Here we report that after denaturation by heat in the presence of 8 M urea, the two strands of the same ds DNA fragment of approximately 1-20-kb size migrate differently in 1 M urea containing agarose gels. The two strands are readily distinguished on Southern blots by ss-specific probes. The different migration of the two strands could be attributed to their different, base composi ...[more]

PMID: 19553189

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