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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: closed (31 December 2022) | Viewed by 3630

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

Published Papers (3 papers)

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Research

Article
Structural Polymorphism of Guanine Quadruplex-Containing Regions in Human Promoters
Int. J. Mol. Sci. 2022, 23(24), 16020; https://doi.org/10.3390/ijms232416020 - 16 Dec 2022
Viewed by 475
Abstract
Intramolecular guanine quadruplexes (G4s) are non-canonical nucleic acid structures formed by four guanine (G)-rich tracts that assemble into a core of stacked planar tetrads. G4-forming DNA sequences are enriched in gene promoters and are implicated in the control of gene expression. Most G4-forming [...] Read more.
Intramolecular guanine quadruplexes (G4s) are non-canonical nucleic acid structures formed by four guanine (G)-rich tracts that assemble into a core of stacked planar tetrads. G4-forming DNA sequences are enriched in gene promoters and are implicated in the control of gene expression. Most G4-forming DNA contains more G residues than can simultaneously be incorporated into the core resulting in a variety of different possible G4 structures. Although this kind of structural polymorphism is well recognized in the literature, there remain unanswered questions regarding possible connections between G4 polymorphism and biological function. Here we report a detailed bioinformatic survey of G4 polymorphism in human gene promoter regions. Our analysis is based on identifying G4-containing regions (G4CRs), which we define as stretches of DNA in which every residue can form part of a G4. We found that G4CRs with higher degrees of polymorphism are more tightly clustered near transcription sites and tend to contain G4s with shorter loops and bulges. Furthermore, we found that G4CRs with well-characterized biological functions tended to be longer and more polymorphic than genome-wide averages. These results represent new evidence linking G4 polymorphism to biological function and provide new criteria for identifying biologically relevant G4-forming regions from genomic data. Full article
(This article belongs to the Special Issue Bioinformatics of Unusual DNA and RNA Structures)
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Article
Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice
Int. J. Mol. Sci. 2022, 23(15), 8404; https://doi.org/10.3390/ijms23158404 - 29 Jul 2022
Viewed by 714
Abstract
DNA G-quadruplexes (G4s) are non-canonical four-stranded DNA structures involved in various biological processes in eukaryotes. Molecularly crowded solutions and monovalent cations have been reported to stabilize in vitro and in vivo G4 formation. However, how K+ and Na+ affect G4 formation [...] Read more.
DNA G-quadruplexes (G4s) are non-canonical four-stranded DNA structures involved in various biological processes in eukaryotes. Molecularly crowded solutions and monovalent cations have been reported to stabilize in vitro and in vivo G4 formation. However, how K+ and Na+ affect G4 formation genome-wide is still unclear in plants. Here, we conducted BG4-DNA-IP-seq, DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing, under K+ and Na+ + PEG conditions in vitro. We found that K+-specific IP-G4s had a longer peak size, more GC and PQS content, and distinct AT and GC skews compared to Na+-specific IP-G4s. Moreover, K+- and Na+-specific IP-G4s exhibited differential subgenomic enrichment and distinct putative functional motifs for the binding of certain trans-factors. More importantly, we found that K+-specific IP-G4s were more associated with active marks, such as active histone marks, and low DNA methylation levels, as compared to Na+-specific IP-G4s; thus, K+-specific IP-G4s in combination with active chromatin features facilitate the expression of overlapping genes. In addition, K+- and Na+-specific IP-G4 overlapping genes exhibited differential GO (gene ontology) terms, suggesting they may have distinct biological relevance in rice. Thus, our study, for the first time, explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future. Full article
(This article belongs to the Special Issue Bioinformatics of Unusual DNA and RNA Structures)
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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
Cited by 3 | Viewed by 1554
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)
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