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The electrophoretic mobility of DNA three-way junctions is affected by the sequence of overhanging single-stranded ends

The electrophoretic mobility of DNA three-way junctions is affected by the sequence of overhanging single-stranded ends
The electrophoretic mobility of DNA three-way junctions is affected by the sequence of overhanging single-stranded ends
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
gel mobility, three-way DNA junctions
0173-0835
413-417
Assenberg, R.
665b7d5b-4bc7-47f6-ba77-17e15d9103d3
Fox, K.R.
9da5debc-4e45-473e-ab8c-550d1104659f
Assenberg, R.
665b7d5b-4bc7-47f6-ba77-17e15d9103d3
Fox, K.R.
9da5debc-4e45-473e-ab8c-550d1104659f

Assenberg, R. and Fox, K.R. (2001) The electrophoretic mobility of DNA three-way junctions is affected by the sequence of overhanging single-stranded ends. Electrophoresis, 22 (3), 413-417. (doi:10.1002/1522-2683(200102)22:3<413::AID-ELPS413>3.0.CO;2-S).

Record type: Article

Abstract

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

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Published date: 1 February 2001
Keywords: gel mobility, three-way DNA junctions

Identifiers

Local EPrints ID: 56037
URI: https://eprints.soton.ac.uk/id/eprint/56037
ISSN: 0173-0835
PURE UUID: 03153507-ca55-4823-8c6a-79ff5fcf5b3e
ORCID for K.R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

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Date deposited: 08 Aug 2008
Last modified: 20 Jul 2019 01:27

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Contributors

Author: R. Assenberg
Author: K.R. Fox ORCID iD

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