NMR dynamics study of the Z-DNA binding domain of human ADAR1 bound to various DNA duplexes

Solution structure of the free Zα domain of human DLM-1 (ZBP1/DAI), a Z-DNA binding domain

“…NMR spectroscopy revealed that Zα ADAR1 is also capable of binding B-DNA and then converting it to Z-DNA, which suggested an active B-Z DNA transition mechanism (Kang et al 2009). Further studies on Zα ADAR1 indicated that it binds Z-DNA using a distinct conformation in a highly flexible region of the protein, the β1-loop-α2 segment, and that Zα ADAR1 undergoes conformational change as it binds B-DNA with lower affinity compared to with Z-DNA (Lee et al 2012). As a homolog of Zα DLM-1, human Zβ DLM-1 has a similar structural fold, but shows significant variation in the sequence of the residues that are essential for Z-DNA binding (Ha et al 2008).…”

Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

“…Instead, the observed k ex value for the imino proton in the B-DNA (not Z-DNA) conformation could be expressed as a function of the relative Z-DNA population ( f Z = Z t /[N] t ) by the following equation: where k ex,B and k ex,BP are the exchange rate constants of the imino protons for free B-DNA and the BP complex, respectively [ 42 ]. The NMR dynamics studies found that hZα ADAR1 binds to non-CG-repeat DNA with weak binding affinity through the α3 helix as well as through the loop-β1-loop (151–158) and the α3-loop-β2 regions (178–191) [ 46 ]. Then, the B-form helix of non-CG-repeat DNA duplexes can be converted to a Z-conformation via these multiple intermolecular interactions with hZα ADAR1 proteins [ 46 ].…”

“…The NMR dynamics studies found that hZα ADAR1 binds to non-CG-repeat DNA with weak binding affinity through the α3 helix as well as through the loop-β1-loop (151–158) and the α3-loop-β2 regions (178–191) [ 46 ]. Then, the B-form helix of non-CG-repeat DNA duplexes can be converted to a Z-conformation via these multiple intermolecular interactions with hZα ADAR1 proteins [ 46 ]. These studies explained how hZα ADAR1 exhibited the sequence preference of d(CGCGCG) 2 >> d(CACGTG) 2 > d(CGTACG) 2 during the B-Z transition [ 42 , 46 ].…”

“…Then, the B-form helix of non-CG-repeat DNA duplexes can be converted to a Z-conformation via these multiple intermolecular interactions with hZα ADAR1 proteins [ 46 ]. These studies explained how hZα ADAR1 exhibited the sequence preference of d(CGCGCG) 2 >> d(CACGTG) 2 > d(CGTACG) 2 during the B-Z transition [ 42 , 46 ]. First, the P binds to the B, with a sequence preference of d(CGCGCG) 2 >> d(CACGTG) 2 > d(CGTACG) 2 [ 42 ], even though the structural features of these three DNA duplexes complexed with hZα ADAR1 are very similar to each other [ 34 ].…”

“…Third, the ZP of d(CGCGCG) 2 and d(CACGTG) 2 binds to the P and forms the stable ZP 2 complex with a sequence preference of d(CGCGCG) 2 >> d(CACGTG) 2 , which acts as the third sequence discrimination step [ 42 ]. Taken together, it was suggested that hZα ADAR1 selectively recognizes the alternating d(CG) n sequence and then converts it to a Z-form helix in long genomic DNA through its multiple sequence discrimination steps [ 42 , 46 ].…”