Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis | Zendy

Éva Hegedüs | Zendy; Endre Kókai | Zendy; Alexander Kotlyar | Zendy; Viktor Dombrádi | Zendy; Gábor Szabó | Zendy

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

Author(s) -

Éva Hegedüs,

Endre Kókai,

Alexander Kotlyar,

Viktor Dombrádi,

Gábor Szabó

Publication year - 2009

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkp539

Subject(s) - agarose , urea , denaturation (fissile materials) , dna , biology , electrophoresis , agarose gel electrophoresis , gel electrophoresis , nucleic acid denaturation , microbiology and biotechnology , biochemistry , base pair , biophysics , chromatography , base sequence , chemistry , nuclear chemistry

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.

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