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Updated: Apr 24, 2026

Visualization of UV-induced Replication Intermediates in E. coli using Two-dimensional Agarose-gel Analysis
Published on: December 21, 2010
Two-dimensional agarose gel electrophoresis for analysis of DNA replication
Sandra K Villwock1, Oscar M Aparicio
1Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
Abstract:
The initiation, elongation, and termination of DNA replication are each associated with distinct, nonlinear DNA structures that can be resolved and identified by two-dimensional (2D) agarose gel electrophoresis. This method involves: isolation of genomic DNA while preserving fragile replication structures, digestion of the DNA with a restriction enzyme, separation of DNA by size and shape through two distinct stages of agarose gel electrophoresis, and Southern blotting to probe for the specific sequence(s) of interest. The method has been most commonly used to determine the activity level of putative replication origin-containing sequences, and has also been used to analyze replication timing, fork progression, fork pausing, fork stalling and collapse, termination, and recombinational repair.
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