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Special Issue "Z-DNA and Z-RNA: From Physical Structure to Biological Function"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (1 October 2021).

Special Issue Editors

Dr. Alan Herbert
E-Mail Website
Guest Editor
Discovery, InsideOutBio, Inc., Charlestown, MA, USA
Interests: Z-DNA; Z-RNA; ADAR; Zα; flipons; genetics; immunology
Special Issues and Collections in MDPI journals
Dr. Maria S. Poptsova
E-Mail Website
Guest Editor
Bioifnformatics Lab, Big Data and Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
Interests: non-B DNA structures; Z-DNA; quadruplexes; triplexes; machine learning; deep learning
Special Issues and Collections in MDPI journals
Dr. Beat Rolf Vögeli
E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
Interests: biophysics; nuclear magnetic resonance; protein and nucleic acid structure and dynamics
Special Issues and Collections in MDPI journals
Dr. Quentin Vicens
E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Genetics, and RNA BioScience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
Interests: biochemistry; cryo-electron microscopy; molecular biology; ribosome; RNA structure and folding; structure prediction; X-ray crystallography
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue will commemorate a half-century of discoveries related to the left-handed Z conformations of DNA and RNA. Such innovations are represented by a wide range of disciplines. Starting with the crystallization of Z-DNA in 1979, biophysical and biochemical studies have yielded many unanticipated and fascinating insights into this class of higher energy nucleic acid conformations.

Recent discoveries of biological functions for left-handed Z-conformations have demonstrated important roles in immunity against infectious agents and cancers. More generally, research on Z conformations underscore the impact of alternative DNA and RNA conformations in both normal cellular function and disease. They further emphasize that regulatory information is encoded by structure in addition to sequence.

This joint Special Issue between two flagship MDPI journals—Molecules and the International Journal of Molecular Sciences—intends to summarize the status of Z-DNA and Z-RNA research. With this collection, we aim to help build collaborations across the many disciplines that study these conformations and their implications in biology.

We invite authors to help develop a roadmap to guide future discoveries by submitting a review at the leading edge of their respective fields, to either Molecules or IJMS, according to their preference as well as journal aims and scopes.

We also wish to encourage all to join us for the first virtual ABZ meeting, which is planned for May 19, 2021 (more on that soon).

Dr. Alan Herbert
Dr. Maria S. Poptsova
Dr. Beat Vögeli
Dr. Quentin Vicens
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ADAR
  • autoimmune disease
  • cancer
  • gene regulation
  • Z-DNA
  • Z-RNA
  • ZBP1
  • Flipons
  • viral immunity
  • base modification
  • topology
  • DNA repeats

Related Special Issue

Published Papers (2 papers)

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Editorial

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Editorial
Special Issue: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA
Int. J. Mol. Sci. 2021, 22(14), 7686; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147686 - 19 Jul 2021
Viewed by 608
Abstract
It is now difficult to believe that a biological function for the left-handed Z-DNA and Z-RNA conformations was once controversial. The papers in this Special Issue, “Z-DNA and Z-RNA: from Physical Structure to Biological Function”, are based on presentations at the ABZ2021 meeting [...] Read more.
It is now difficult to believe that a biological function for the left-handed Z-DNA and Z-RNA conformations was once controversial. The papers in this Special Issue, “Z-DNA and Z-RNA: from Physical Structure to Biological Function”, are based on presentations at the ABZ2021 meeting that was held virtually on 19 May 2021 and provide evidence for several biological functions of these structures. The first of its kind, this international conference gathered over 200 scientists from many disciplines to specifically address progress in research involving Z-DNA and Z-RNA. These high-energy left-handed conformers of B-DNA and A-RNA are associated with biological functions and disease outcomes, as evidenced from both mouse and human genetic studies. These alternative structures, referred to as “flipons”, form under physiological conditions, regulate type I interferon responses and induce necroptosis during viral infection. They can also stimulate genetic instability, resulting in adaptive evolution and diseases such as cancer. The meeting featured cutting-edge science that was, for the most part, unpublished. We plan for the ABZ meeting to reconvene in 2022. Full article
(This article belongs to the Special Issue Z-DNA and Z-RNA: From Physical Structure to Biological Function)

Research

Jump to: Editorial

Article
The Binding of Monoclonal and Polyclonal Anti-Z-DNA Antibodies to DNA of Various Species Origin
Int. J. Mol. Sci. 2021, 22(16), 8931; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22168931 - 19 Aug 2021
Viewed by 444
Abstract
DNA is a polymeric macromolecule that can display a variety of backbone conformations. While the classical B-DNA is a right-handed double helix, Z-DNA is a left-handed helix with a zig-zag orientation. The Z conformation depends upon the base sequence, base modification and supercoiling [...] Read more.
DNA is a polymeric macromolecule that can display a variety of backbone conformations. While the classical B-DNA is a right-handed double helix, Z-DNA is a left-handed helix with a zig-zag orientation. The Z conformation depends upon the base sequence, base modification and supercoiling and is considered to be transient. To determine whether the presence of Z-DNA can be detected immunochemically, the binding of monoclonal and polyclonal anti-Z-DNA antibodies to a panel of natural DNA antigens was assessed by an ELISA using brominated poly(dG-dC) as a control for Z-DNA. As these studies showed, among natural DNA tested (Micrococcus luteus, calf thymus, Escherichiacoli, salmon sperm, lambda phage), micrococcal (MC) DNA showed the highest binding with both anti-Z-DNA preparations, and E. coli DNA showed binding with the monoclonal anti-DNA preparation. The specificity for Z-DNA conformation in MC DNA was demonstrated by an inhibition binding assay. An algorithm to identify propensity to form Z-DNA indicated that DNA from Mycobacterium tuberculosis could form Z-DNA, a prediction confirmed by immunoassay. Together, these findings indicate that anti-Z-DNA antibodies can serve as probes for the presence of Z-DNA in DNA of various species origin and that the content of Z-DNA varies significantly among DNA sources. Full article
(This article belongs to the Special Issue Z-DNA and Z-RNA: From Physical Structure to Biological Function)
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