ArticleNucleic acids research2021
Sequence-dependent cost for Z-form shapes the torsion-driven B-Z transition via close interplay of Z-DNA and DNA bubble.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Z-nucleic acid-mediated PANoptosis in infection, inflammation, and cancer.Communications biology · 2026Review
- Formation and biological implications of Z-DNA.Trends in genetics : TIG · 2026Review
- Z-DNA Hunter tool for straightforward detection of Z-DNA forming regions and a case study inNAR genomics and bioinformatics · 2025Article
- Global identification and functional characterization of Z-DNA in rice.Plant biotechnology journal · 2025Article
- Z-form DNA-RNA hybrid blocks DNA replication.Nucleic acids research · 2025Article
- Computational Simulation and Biophysical Study on Cerium Chloride-Induced B-to-Z Transition in (CG)ACS omega · 2024Article
- Dynamic alternative DNA structures in biology and disease.Nature reviews. Genetics · 2023Review
- A shared 'vulnerability code' underpins varying sources of DNA damage throughout paternal germline transmission in mouse.Nucleic acids research · 2023Article
- Single-Molecule Methods to Study Z-DNA Mechanics and Dynamics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- DNA Bending Force Facilitates Z-DNA Formation under Physiological Salt Conditions.Journal of the American Chemical Society · 2022Article
- Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle?Biomolecules · 2022Review
- Mono a Mano: ZBP1's Love-Hate Relationship with the Kissing Virus.International journal of molecular sciences · 2022Review
- Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo.Molecular cell · 2022Review
- Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair.Frontiers in bioengineering and biotechnology · 2022Review
- Special Issue: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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