The Zα domain from human ADAR1 binds to the Z-DNA conformer of many different sequences

Z-DNA, the left-handed conformer of DNA, is stabilized by the negative supercoiling generated during the movement of an RNA polymerase through a gene. Recently, we have shown that the editing enzyme ADAR1 (double-stranded RNA adenosine deaminase, type 1) has two Z-DNA binding motifs, Z alpha and Z beta, the function of which is currently unknown. Here we show that a peptide containing the Z alpha motif binds with high affinity to Z-DNA as a dimer, that the binding site is no larger than 6 bp and that the Z alpha domain can flip a range of sequences, including d(TA)(3), into the Z-DNA conformation. Evidence is also presented to show that Z alpha and Z beta interact to form a functional DNA binding site. Studies with atomic force microscopy reveal that binding of Z alpha to supercoiled plasmids is associated with relaxation of the plasmid. Pronounced kinking of DNA is observed, and appears to be induced by binding of Z alpha. The results reported here support a model where the Z-DNA binding motifs target ADAR1 to regions of negative supercoiling in actively transcribing genes. In this situation, binding by Z alpha would be dependent upon the local level of negative superhelicity rather than the presence of any particular sequence.