The Z-DNA binding domain of human ADAR1 (Z alpha(ADAR1)) preferentially binds Z-DNA rather than B-DNA with high binding affinity. Here, we have carried out chemical shift perturbation and backbone dynamics studies of Z alpha(ADAR1) in the free form and in complex with three DNA duplexes, d(CGCGCG)(2), d(CACGTG)(2), and d(CGTACG)(2). This study reveals that Z alpha(ADAR1) initially binds to d(CGCGCG)(2) through the distinct conformation, especially in the unusually flexible beta 1-loop-alpha 2 region, from the d(CGCGCG)(2)-(Z alpha(ADAR1))(2) complex. This study also suggests that Z alpha(ADAR1) exhibits a distinct conformational change during the B-Z transition of non-CG-repeat DNA duplexes with low binding affinities compared to the CG-repeat DNA duplex. 2012 Elsevier Inc. All rights reserved.