NMR study on the B-Z junction formation of DNA duplexes induced by Z-DNA binding domain of human ADAR1

Yeon Mi Lee, Hee Eun Kim, Chin Ju Park, Ae Ree Lee, Hee Chul Ahn, Sung Jae Cho, Kwang Ho Choi, Byong Seok Choi, Joon Hwa Lee

Research output: Contribution to journalArticlepeer-review

30 Scopus citations

Abstract

Z-DNA is produced in a long genomic DNA by Z-DNA binding proteins, through formation of two B-Z junctions with the extrusion of one base pair from each junction. To answer the question of how Z-DNA binding proteins induce B-Z transitions in CG-rich segments while maintaining the B-conformation of surrounding segments, we investigated the kinetics and thermodynamics of base-pair openings of a 13-bp DNA in complex with the Z-DNA binding protein, Zα ADAR1. We also studied perturbations in the backbone of Zα ADAR1 upon binding to DNA. Our study demonstrates the initial contact conformation as an intermediate structure during B-Z junction formation induced by Zα ADAR1, in which the Zα ADAR1 protein displays unique backbone conformational changes, but the 13-bp DNA duplex maintains the B-form helix. We also found the unique structural features of the 13-bp DNA duplex in the initial contact conformation: (i) instability of the AT-rich region II and (ii) longer lifetime for the opening state of the CG-rich region I. Our findings suggest a three-step mechanism of B-Z junction formation: (i) Zα ADAR1 specifically interacts with a CG-rich DNA segment maintaining B-form helix via a unique conformation; (ii) the neighboring AT-rich region becomes very unstable, and the CG-rich DNA segment is easily converted to Z-DNA; and (iii) the AT-rich regions are base-paired again, and the B-Z junction structure is formed.

Original languageEnglish
Pages (from-to)5276-5283
Number of pages8
JournalJournal of the American Chemical Society
Volume134
Issue number11
DOIs
StatePublished - 21 Mar 2012

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