Open AccessThe Zalpha domain from human ADAR1 binds to the Z-DNA conformer of many different sequences
Author(s) -
Alan Herbert,
Markus Schade,
Ky Lowenhaupt,
Jens Alfken,
Thomas Schwartz,
Luda S. Shlyakhtenko,
Yuri L. Lyubchenko,
Alexander Rich
Publication year - 1998
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/26.15.3486
Subject(s) - dna supercoil , biology , dna , binding site , binding domain , hmg box , rna , microbiology and biotechnology , dna clamp , dna binding site , biophysics , gene , biochemistry , dna binding protein , dna replication , gene expression , transcription factor , promoter , reverse transcriptase
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, Zalpha and Zbeta, the function of which is currently unknown. Here we show that a peptide containing the Zalpha motif binds with high affinity to Z-DNA as a dimer, that the binding site is no larger than 6 bp and that the Zalpha domain can flip a range of sequences, including d(TA)3, into the Z-DNAconformation. Evidence is also presented to show that Zalpha and Zbeta interact to form a functional DNA binding site. Studies with atomic force microscopy reveal that binding of Zalpha to supercoiled plasmids is associated with relaxation of the plasmid. Pronounced kinking of DNA is observed, and appears to be induced by binding of Zalpha. 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 Zalpha would be dependent upon the local level of negative superhelicity rather than the presence of any particular sequence.