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Unusual DNA and RNA Structures: 2nd Edition

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

Deadline for manuscript submissions: 30 October 2025 | Viewed by 1527

Special Issue Editors


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Guest Editor
Department of Biology and Ecology, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic
Interests: G-quadruplexes; triplexes; Z-DNA/RNA; DNA cruciforms; i-motifs; bioinformatics; biophysical methods
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Special Issue Information

Dear Colleagues,

It is our great pleasure to open this Special Issue focused on unusual DNA and RNA structures. As you may know, it is a follow-up of the currently closed and successful special issue entitled Bioinformatics of Unusual DNA and RNA Structures (https://www.mdpi.com/journal/ijms/special_issues/Unusual_DNA_RNA). Here, we would like to extend the original focus also on the wet-lab methods for researching unusual DNA and RNA structures comprising G-quadruplexes, i-motifs, DNA triplexes, R-loops, Z-DNA/Z-RNA, A-DNA, cruciforms, and maybe still undescribed structural entities.

Because this field of science is evolving rapidly, there is a need for integrative approaches that allow us to evaluate/generalize our knowledge about unusual DNA and RNA structures. The topics of this Special Issue include, but are not limited to:

  • Computational analyses of unusual DNA- and RNA-forming motifs occurring in genomes and comparative analyses of these motifs between species
  • New computational methods and tools for unusual DNA- and RNA-forming motifs (and structures) prediction and analysis
  • Wet-lab methods related to all possible aspects of unusual DNA and RNA structures (both biophysical and in situ/in vivo experiments)
  • Interaction of unusual DNA and RNA structures with proteins and other biomacromolecules
  • Structural studies of unusual DNA and RNA structures including both in vitro (RTG crystallography, NMR, cryo-EM) and in silico (molecular dynamics) studies
  • Screening and analyses of potential small ligands stabilizing/destabilizing unusual DNA and RNA structures, drug discovery
  • Unusual DNA and RNA structures in human health and diseases
  • Unusual DNA and RNA structures in plants (and agriculture)
  • Genome-wide association studies (GWAS) to find links between unusual DNA- and RNA-forming motifs and phenotypes/diseases

Original investigations (both full articles and short communications), as well as concise review manuscripts, from experts in the relevant research fields, will be considered for publication. As guest editors, we guarantee a fair and constructive peer-review process for your submitted articles.

Dr. Martin Bartas
Dr. Petr Pečinka
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 submissions that pass pre-check are 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

  • G-quadruplex
  • i-motifs
  • R-loops
  • Z-DNA
  • A-DNA
  • cruciforms
  • nucleic acid structures

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Published Papers (1 paper)

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Research

16 pages, 7976 KiB  
Article
Role of R-Loop Structure in Efficacy of RNA Elongation Synthesis by RNA Polymerase from Escherichia coli
by Nadezhda A. Timofeyeva, Ekaterina I. Tsoi, Darya S. Novopashina, Aleksandra A. Kuznetsova and Nikita A. Kuznetsov
Int. J. Mol. Sci. 2024, 25(22), 12190; https://doi.org/10.3390/ijms252212190 - 14 Nov 2024
Viewed by 1084
Abstract
The mechanism of transcription proceeds through the formation of R-loop structures containing a DNA–RNA heteroduplex and a single-stranded DNA segment that should be placed inside the elongation complex; therefore, these nucleic acid segments are limited in length. The attachment of each nucleotide to [...] Read more.
The mechanism of transcription proceeds through the formation of R-loop structures containing a DNA–RNA heteroduplex and a single-stranded DNA segment that should be placed inside the elongation complex; therefore, these nucleic acid segments are limited in length. The attachment of each nucleotide to the 3′ end of an RNA strand requires a repeating cycle of incoming nucleoside triphosphate binding, catalysis, and enzyme translocation. Within these steps of transcription elongation, RNA polymerase sequentially goes through several states and is post-translocated, catalytic, and pre-translocated. Moreover, the backward movement of the polymerase, which is essential for transcription pausing and proofreading activity, gives rise to a backtracked state. In the present study, to analyze both the efficacy of transcription elongation complex (TEC) formation and the rate of RNA synthesis, we used a set of model R-loops that mimic the pre-translocated state, post-translocated state, backtracked state, and a misincorporation event. It was shown that TEC assembly proceeds as an equilibrium process, including the simultaneous formation of a catalytically competent TEC as well as a catalytically inactive conformation. Our data suggest that the inactive complex of RNA polymerase with an R-loop undergoes slow conformational changes, resulting in a catalytically competent TEC. It was revealed that the structural features of R-loops affect the ratio between active and inactive states of the TEC, the rate of conformational rearrangements required for the induced-fit transition from the inactive state to the catalytically competent TEC, and the rates of accumulation of both the total RNA products and long RNA products. Full article
(This article belongs to the Special Issue Unusual DNA and RNA Structures: 2nd Edition)
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