A NOVEL TYPE OF INTERACTION BETWEEN CRUCIFORM DNA AND A CRUCIFORM BINDING-PROTEIN FROM HELA-CELLS

We recently identified and enriched a protein (CBP) from HeLa cells wi th binding specificity for cruciform-containing DNA. We have now studi ed the interaction of CBP with stable cruciform DNA molecules containi ng the 27 bp palindrome of SV40 on one strand and an unrelated 26 bp p alindrome on the other strand by hydroxyl radical footprinting. The CB P-DNA interaction is localized to the four-way junction at the base of the cruciforms. CBP appears to interact with the elbows of the juncti ons in an asymmetric fashion. Upon CBP binding, structural distortions were observed in the cruciform stems and in a DNA region adjacent to the junction. These features distinguish CBP from other cruciform bind ing proteins, which bind symmetrically and display exclusively either contacts with the DNA backbone or structural alterations in the DNA.