Many proteins involved in DNA repair systems interact with DNA that has 
structure altered from the typical B-form helix. Using magnetic beads to 
immobilize DNAs containing various types of structures, we evaluated the in 
vitro binding activities of two well-characterized DNA repair proteins, 
Escherichia coli MutS and human p53. E. coli MutS bound to double-stranded DNAs, 
with higher affinity for a G/T mismatch compared to a G/A mismatch and highest 
affinity for larger non-B-DNA structures. E. coli MutS bound best to DNA between 
pH 6 and 9. Experiments discriminated between modes of p53-DNA binding, and 
increasing ionic strength reduced p53 binding to nonspecific double-stranded 
DNA, but had minor effects on binding to consensus response sequences or 
single-stranded DNA. Compared to nonspecific DNA sequences, p53 bound with a 
higher affinity to mismatches and base insertions, while binding to various 
hairpin structures was similar to that observed to its consensus DNA sequence. 
For hairpins containing CTG repeats, the extent of p53 binding was proportional 
to the size of the repeat. In summary, using the flexibility of the magnetic 
bead separation assay we demonstrate that pH and ionic strength influence the 
binding of two DNA repair proteins to a variety of DNA structures.