ijms-logo

Journal Browser

Journal Browser

Special Issue "Bioinformatics of Unusual DNA and RNA Structures"

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

Deadline for manuscript submissions: 31 March 2022.

Special Issue Editors

Dr. Petr Pečinka
E-Mail Website
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
Dr. Vaclav Brazda
E-Mail Website
Guest Editor
Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
Interests: relationship between DNA structure and function; interaction of proteins with DNA, local DNA structures and DNA damage; p53 protein and carcinogenesis; bioinformatics; immunology; neurosciences; neurodegeneration
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is our great pleasure to open this Special Issue focused on all aspects of unusual DNA and RNA structures, mainly from the bioinformatical point of view. By unusual DNA and RNA structures, we mean primarily G-quadruplexes, i-motifs, triplexes, Z-DNA/RNA, DNA cruciforms, R-loops, RNA hairpins, etc. They are called “unusual”, but in fact, it is evident now, that they are broadly presented in the genomes of all living organisms, as well as viruses, playing important roles in the regulation of various molecular processes. Because this field of science is evolving rapidly, there is a need for integrative computational approaches allowing 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 DNA- and RNA-forming motifs occurring in genomes (in general)
  • Comparative analyses of DNA- and RNA-forming motifs between species (from an evolutionarily point of view)
  • New computational methods and tools for DNA- and RNA-forming motifs prediction and analysis
  • Genome-wide association studies (GWAS) to find links between these DNA- and RNA-forming motifs and phenotypes/diseases
  • Structural studies of DNA and RNA high-order structures (molecular docking, dynamics simulation, etc.)
  • Screening and analyses of potential small ligands stabilizing/destabilizing DNA and RNA structures
  • Interaction of proteins with unusual DNA and RNA structures

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. Petr Pečinka
Dr. Vaclav Brazda
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

  • G-quadruplex
  • i-motif
  • triplex
  • Z-DNA
  • cruciforms
  • bioinformatics
  • 3D-modeling
  • ligand docking
  • algorithms
  • computational biology

Published Papers (1 paper)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Article
R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences
Int. J. Mol. Sci. 2021, 22(23), 12857; https://doi.org/10.3390/ijms222312857 - 27 Nov 2021
Viewed by 401
Abstract
R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as [...] Read more.
R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes. Full article
(This article belongs to the Special Issue Bioinformatics of Unusual DNA and RNA Structures)
Show Figures

Figure 1

Back to TopTop