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Updated: Jun 8, 2026

Visualization of UV-induced Replication Intermediates in E. coli using Two-dimensional Agarose-gel Analysis

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Published on: December 21, 2010

5'-Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocase.

Eric J Tomko¹, Haifeng Jia, Jeehae Park

¹Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA.

The EMBO Journal

|September 30, 2010

Summary

Escherichia coli UvrD protein acts as a DNA helicase or translocase. Monomeric UvrD specifically binds 5’ single-stranded DNA junctions, enabling translocation, while 3’ junctions inhibit its activity.

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Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair

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Published on: May 24, 2017

Area of Science:

Molecular Biology
Biochemistry
Genetics

Background:

Escherichia coli UvrD is a crucial superfamily 1A helicase/translocase.
UvrD exhibits dual functionality as a helicase or single-stranded DNA (ssDNA) translocase.
Oligomeric state dictates UvrD activity: monomer for ssDNA translocation, dimer for helicase activity.

Purpose of the Study:

Investigate the binding specificity of monomeric UvrD to different DNA structures.
Determine the role of DNA junction architecture in modulating UvrD's translocase and helicase functions.
Elucidate the structural basis for UvrD's junction specificity.

Main Methods:

In vitro biochemical assays to assess UvrD binding and translocation.
Site-directed mutagenesis to probe the role of the 2B subdomain.
Analysis of UvrD interaction with various DNA substrates, including 5' and 3' ssDNA-duplex junctions.

Main Results:

Monomeric UvrD exhibits high-affinity binding and translocation initiation at 5'-ssDNA-duplex junctions.
Conversely, 3'-ssDNA-duplex junctions inhibit both translocase and helicase activities of monomeric UvrD.
The 2B subdomain of UvrD is critical for discerning junction specificity.

Conclusions:

A functional separation exists between UvrD's helicase and translocase activities.
Monomeric UvrD can be selectively loaded onto 5'-ssDNA junctions for translocation-dependent processes.
This finding provides insights into the regulation of DNA repair and replication pathways involving UvrD.