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Sequence-dependent cost for Z-form shapes the torsion-driven B-Z transition via close interplay of Z-DNA and DNA bubble

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Title
Sequence-dependent cost for Z-form shapes the torsion-driven B-Z transition via close interplay of Z-DNA and DNA bubble
Author(s)
Sook Ho Kim; Hae Jun Jung; Il-Buem Lee; Nam-Kyung Lee; Seok-Cheol Hong
Publication Date
2021-04
Journal
NUCLEIC ACIDS RESEARCH, v.49, no.7, pp.3651 - 3660
Publisher
OXFORD UNIV PRESS
Abstract
Despite recent genome-wide investigations of functional DNA elements, the mechanistic details about their actions remain elusive. One intriguing possibility is that DNA sequences with special patterns play biological roles, adopting non-B-DNA conformations. Here we investigated dynamics of thymine-guanine (TG) repeats, microsatellite sequences and recurrently found in promoters, as well as cytosine-guanine (CG) repeats, best-known Z-DNA forming sequence, in the aspect of Z-DNA formation. We measured the energy barriers of the B-Z transition with those repeats and discovered the sequence-dependent penalty for Z-DNA generates distinctive thermodynamic and kinetic features in the torque-induced transition. Due to the higher torsional stress required for Z-form in TG repeats, a bubble could be induced more easily, suppressing Z-DNA induction, but facilitate the B-Z interconversion kinetically at the transition midpoint. Thus, the Z-form by TG repeats has advantages as a torsion buffer and bubble selector while the Z-form by CG repeats likely behaves as torsion absorber. Our statistical physics model supports quantitatively the populations of Z-DNA and reveals the pivotal roles of bubbles in state dynamics. All taken together, a quantitative picture for the transition was deduced within the close interplay among bubbles, plectonemes and Z-DNA.
URI
https://pr.ibs.re.kr/handle/8788114/9794
DOI
10.1093/nar/gkab153
ISSN
0305-1048
Appears in Collections:
Center for Molecular Spectroscopy and Dynamics(분자 분광학 및 동력학 연구단) > 1. Journal Papers (저널논문)
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