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The electrophoretic mobility of DNA three‐way junctions is affected by the sequence of overhanging single‐stranded ends
Author(s) -
Assenberg René,
Fox Keith R.
Publication year - 2001
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/1522-2683(200102)22:3<413::aid-elps413>3.0.co;2-s
Subject(s) - restriction enzyme , electrophoresis , dna , sequence (biology) , gel electrophoresis , endonuclease , chemistry , biophysics , biology , biochemistry
The folding of three‐ and four‐way DNA junctions is often assessed by comparing the electrophoretic mobility of restriction enzyme fragments, using the long‐short arm assay. We have compared the mobility of synthetic three‐way junctions that contain identical branch point sequences, but different restriction sites in the arms. We show that the mobility of fragments is affected by the sequence of the overhanging ends. In general, GC‐rich overhangs produce fragments with anomalous mobilities. These anomalies can be prevented by treating the cleaved junctions with mung bean endonuclease, elevating the electrophoresis temperature or using blunt cleaving restriction endonucleases.