Structural studies of B-Z junction
Recent researches reveal the presence of Z-DNA in vivo. Especially, the Z-DNA is more frequently detect near by transcription start site than other regions of genome. Since the Z-DNA is high energy conformation of the DNA, stabilization of Z-DNA requires the energy. The negative supercoiling, movement of RNA polymerase, and binding of Z-DNA binding proteins stabilize the Z-DNA in vivo. Hence the Z-DNA forms in the genomic DNA, the Z-DNA should be found with B conformation of DNA. The result of formation of Z-DNA between B-DNA induces formation of junctional structure. Ha et. al. reveals the junction structure of B-DNA and Z-DNA. The crystal structure of B-Z junction shows that junction adopts the base extruded structure (Fig. 1). While the crystal structure of B-Z junction has been solved, the possible variety of junction structure in biological system is still not studied yet. The CpG islands in promoter region are consist of Z-DNA favorable sequence which is alteration of purine and pyrimidine. The variety of sequence in promoter region could support the hypothesis which the structure of B-Z junction could be variable. Therefore, we design the sequences which are favorable to make B-Z junction with Z-DNA binding protein and intent to solve the each structures.
 
Base Flipping in Z-form-containing Helical Junction
Base flipping is a major structural feature in the B-Z DNA junction. At the B-Z junction, two bases are excluded from the base pairing at the junction and flipped. Despite the established role of base flipping at the B-Z junction, it remains unanswered if the same base flipping applies to other types of Z-DNA-containing junctions. To address whether base flipping is a prevalent feature for various Z-DNA-containing junctions: B-Z, A-Z and Z-Z junctions. By monitoring fluorescently labeled 2-aminoadenine at various positions relative to the junction point, we show that base flipping occurs not only in the B-Z junction but also in the A-Z and Z-Z junctions. Our data suggest that base flipping is a general characteristic for Z-DNA-containing junctions.
 
Activation mechanisms of Z-DNA binding proteins by Z-DNA binding
All known Z-DNA binding proteins except viral E3L proteins have paired Z-DNA binding domains named Zα and Zβ respectively. These Z-DNA binding proteins are involved in innate immune response. However, reconition mechanisms and activation mechanisms of each Z-DNA binding proteins are yet to be studied. We are concerning about elucidating the activation mechanisms of Z-DNA binding proteins by biochemical studies and structural studies.