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Interactions of yeast HMO2 with distorted DNA

High mobility group proteins are non‐histone nuclear proteins that play a role in DNA repair. The functional roles of HMO2, an HMGB homolog from yeast, were studied by substituting a valine in box A with an alanine. Sequence alignment predicts that this residue intercalates between DNA base pairs. A binding assay with linear DNA showed that the mutant protein has lower binding affinity compared to wild type HMO2, while both mutant and wild type proteins have similar affinity for supercoiled DNA. Both wild‐type and mutant protein were able to protect free DNA ends from exonuclease digestion, suggesting that the substitution does not affect the preferred binding to DNA ends. Assays involving DNA with 2 loops that were seven and nine base pairs apart showed that HMO2 preferred binding to the latter; the 9 bp distance between loops is apparently optimal for HMO2 binding. In a competition assay involving HMO2, supercoiled DNA was able to compete for DNA with 2 loops (9 bp apart) while linear DNA was not. Evidently, the valine in HMO2 box A is important to the protein's ability to bind to linear DNA while its substitution does not alter the preferred binding of HMO2 to DNA ends or to DNA with distortions.