Biological significance of the human protein that specifically binds to triplex DNA

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We have purified a human protein which specifically binds to triplex DNA.To obtain an insight into the function of this protein, we developed a method (Mg^<2+>-dependent triplex affinity capture) to enrich and clone the potential substrates for this protein from human genomic DNA.This procedure utilizes Mg^<2+> for triplex DNA formation between oligonucleotide probes and double-stranded genomic DNA.First, we obtained a library of clones containing poly (dA) ・poly (dT) tracts, which is a component of poly (dT) ・poly (dA) ・poly (dT) triplex, one of the most studied triplex DNA species. We observed the instability of plasmids containing these tracts in E.coli, which is likely to be caused by triplex formation. In the next step, we cloned genomic DNA fragments containing poly (dG-dA) ・poly (dC-dT) tracts, a component of poly (dG-dA) ・poly (dG-dA) ・poly (dC-dT) triplex. The analysis of the clones from the library revealed that these tracts were unstable in the genomic DNA and showed polymorphism among individuals as well as between cells from cancer and normal tissues.