Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease

Area of Science:

• Molecular Biology
• Structural Biology
• Biochemistry

Background:

• Structure-selective endonucleases are crucial for DNA repair and genome stability.
• Slx1 is a unique endonuclease capable of cleaving various branched DNA structures near the branch point.

Purpose of the Study:

• To elucidate the unknown mechanism behind Slx1's broad substrate specificity.
• To structurally and biochemically characterize fungal Slx1's interaction with branched DNA.

Main Methods:

• X-ray crystallography and biochemical assays were used to investigate fungal Slx1.
• Computational modeling was employed to visualize Slx1-DNA interactions.

Main Results:

• A new protein interface on Slx1 that binds the non-cleaved arm of branched DNA was identified.
• DNA binding induces a disorder-to-order transition near the active site, suggesting a regulatory mechanism.
• Models revealed Slx1 bends DNA, localizing the branch point and enabling cleavage away from the 3' end.

Conclusions:

• Slx1 employs a unique DNA-binding interface and DNA bending to achieve broad specificity for branched DNA structures.
• A regulatory mechanism ensures cleavage only occurs when the non-cleaved arm is properly bound.
• This study provides insights into the structure-function relationship of Slx1 in DNA processing.