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Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

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Related Experiment Video

Updated: May 15, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Structural basis of DNA loop recognition by endonuclease V.

Ida Rosnes¹, Alexander D Rowe, Erik S Vik

¹Department of Microbiology, Oslo University Hospital, Rikshospitalet, P.O. Box 4950, Nydalen, N-0424 Oslo, Norway.

Structure (London, England : 1993)

|January 15, 2013

Summary

Endonuclease V (EndoV) uses a unique mechanism involving a DNA-separating wedge and a base recognition pocket to cleave distorted DNA structures, including those with loops. This structural insight reveals a novel DNA repair pathway.

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Last Updated: May 15, 2026

Studying DNA Looping by Single-Molecule FRET

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Published on: June 28, 2014

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

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

Published on: May 24, 2017

Area of Science:

Biochemistry
Structural Biology
DNA Repair Mechanisms

Background:

Endonuclease V (EndoV) is a DNA repair enzyme known to process deaminated adenine (hypoxanthine) and DNA with helical distortions.
Understanding the precise molecular mechanisms by which EndoV recognizes and cleaves distorted DNA structures is crucial for elucidating its role in genome stability.

Purpose of the Study:

To determine the crystal structure of Thermotoga maritima EndoV in complex with DNA containing a one-nucleotide loop.
To elucidate the molecular basis of EndoV's recognition and incision of DNA structures with helical distortions.

Main Methods:

X-ray crystallography was employed to solve the structure of EndoV bound to a DNA substrate containing a one-nucleotide loop.
Structural analysis focused on the interaction between EndoV and the distorted DNA region.

Main Results:

The crystal structure revealed a strand-separating wedge critical for recognizing DNA loop distortions, precisely separating the DNA strands at the distortion site.
The loop nucleotide is positioned on the wedge surface, while the opposite base is flipped into a recognition pocket.
This reveals a distinct mechanism for DNA loop recognition and cleavage mediated by the wedge and base pocket.

Conclusions:

EndoV utilizes a novel mechanism involving a DNA-intercalating wedge and a base pocket for recognizing and cleaving distorted DNA.
This coordinated action facilitates strand incision at helical distortions, offering new insights into DNA repair pathways.