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Molecular Research on RNA Structure
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Molecular Research on RNA Structure

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

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 8685

Special Issue Editor

Dr. Marta Szabat

E-Mail Website
Guest Editor
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, 61-704 Poznań, Poland
Interests: DNA structure; RNA structure; thermodynamics; influenza A virus
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The structures and functions of RNAs gaining more and more interest, it involves in almost all aspects of cell physiology as well as disease development. RNA is a single-stranded polymer composed of only four nucleotides, it possesses an intrinsic ability to fold into complex secondary and tertiary structures, further modulated by post-transcriptional modifications and interaction with ligands (proteins, small metabolites, etc.). The functional diversity of RNA comes from its structural richness.

This Special Issue aims to cover all kinds of studies focus on RNA structure and its role in biological processes. We welcome original research articles and review papers, including (but not limited to) the following topics:

  • The prediction of RNA structure;
  • The interaction with other RNAs or proteins;
  • Characterization of the RNA secondary and tertiary structure in relation to its role in cellular processes
  • Influence of RNA modifications on RNA structure and function
  • Role of RNA structure in disease development
  • Structural study of RNA molecules in complex with small compounds, drugs, and proteins
  • Modulation of RNA structure and function using synthetic biology approaches

Dr. Marta Szabat
Guest Editor

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.

Published Papers (5 papers)

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Research

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23 pages, 3140 KiB  
Article
Structural Characteristics of the 5′-Terminal Region of Mouse p53 mRNA and Identification of Proteins That Bind to This mRNA Region
by Joanna Szpotkowska, Kamil Szpotkowski and Jerzy Ciesiołka
Int. J. Mol. Sci. 2022, 23(17), 9709; https://doi.org/10.3390/ijms23179709 - 26 Aug 2022
Cited by 2 | Viewed by 1462
Abstract
A mouse model has often been used in studies of p53 gene expression. Detailed interpretation of functional studies is, however, hampered by insufficient knowledge of the impact of mouse p53 mRNA’s structure and its interactions with proteins in the translation process. In particular, [...] Read more.
A mouse model has often been used in studies of p53 gene expression. Detailed interpretation of functional studies is, however, hampered by insufficient knowledge of the impact of mouse p53 mRNA’s structure and its interactions with proteins in the translation process. In particular, the 5′-terminal region of mouse p53 mRNA is an important region which takes part in the regulation of the synthesis of p53 protein and its N-truncated isoform Δ41p53. In this work, the spatial folding of the 5′-terminal region of mouse p53 mRNA and its selected sub-fragments was proposed based on the results of the SAXS method and the RNAComposer program. Subsequently, RNA-assisted affinity chromatography was used to identify proteins present in mouse fibroblast cell lysates that are able to bind the RNA oligomer, which corresponds to the 5′-terminal region of mouse p53 mRNA. Possible sites to which the selected, identified proteins can bind were proposed. Interestingly, most of these binding sites coincide with the sites determined as accessible to hybridization of complementary oligonucleotides. Finally, the high binding affinity of hnRNP K and PCBP2 to the 5′-terminal region of mouse p53 mRNA was confirmed and their possible binding sites were proposed. Full article
(This article belongs to the Special Issue Molecular Research on RNA Structure)
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16 pages, 2179 KiB  
Article
A Structural Potential of Rare Trinucleotide Repeat Tracts in RNA
by Dorota Magner, Rafal Nowak, Elzbieta Lenartowicz Onyekaa, Anna Pasternak and Ryszard Kierzek
Int. J. Mol. Sci. 2022, 23(10), 5850; https://doi.org/10.3390/ijms23105850 - 23 May 2022
Viewed by 1516
Abstract
Among types of trinucleotide repeats, there is some disproportion in the frequency of their occurrence in the human exome. This research presents new data describing the folding and thermodynamic stability of short, tandem RNA repeats of 23 types, focusing on the rare, yet [...] Read more.
Among types of trinucleotide repeats, there is some disproportion in the frequency of their occurrence in the human exome. This research presents new data describing the folding and thermodynamic stability of short, tandem RNA repeats of 23 types, focusing on the rare, yet poorly analyzed ones. UV-melting experiments included the presence of PEG or potassium and magnesium ions to determine their effect on the stability of RNA repeats structures. Rare repeats predominantly stayed single-stranded but had the potential for base pairing with other partially complementary repeat tracts. A coexistence of suitably complementary repeat types in a single RNA creates opportunities for interaction in the context of the secondary structure of RNA. We searched the human transcriptome for model RNAs in which different, particularly rare trinucleotide repeats coexist and selected the GABRA4 and CHIC1 RNAs to study intramolecular interactions between the repeat tracts that they contain. In vitro secondary structure probing results showed that the UAA and UUG repeat tracts, present in GABRA4 3′ UTR, form a double helix, which separates one of its structural domains. For the RNA CHIC1 ORF fragment containing four short AGG repeat tracts and the CGU tract, we proved the formation of quadruplexes that blocked reverse transcription. Full article
(This article belongs to the Special Issue Molecular Research on RNA Structure)
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17 pages, 4728 KiB  
Article
RNA and Protein Determinants Mediate Differential Binding of miRNAs by a Viral Suppressor of RNA Silencing Thus Modulating Antiviral Immune Responses in Plants
by Robert Pertermann, Ralph Peter Golbik, Selvaraj Tamilarasan, Torsten Gursinsky, Selma Gago-Zachert, Vitantonio Pantaleo, Iris Thondorf and Sven-Erik Behrens
Int. J. Mol. Sci. 2022, 23(9), 4977; https://doi.org/10.3390/ijms23094977 - 29 Apr 2022
Cited by 2 | Viewed by 1906
Abstract
Many plant viruses express suppressor proteins (VSRs) that can inhibit RNA silencing, a central component of antiviral plant immunity. The most common activity of VSRs is the high-affinity binding of virus-derived siRNAs and thus their sequestration from the silencing process. Since siRNAs share [...] Read more.
Many plant viruses express suppressor proteins (VSRs) that can inhibit RNA silencing, a central component of antiviral plant immunity. The most common activity of VSRs is the high-affinity binding of virus-derived siRNAs and thus their sequestration from the silencing process. Since siRNAs share large homologies with miRNAs, VSRs like the Tombusvirus p19 may also bind miRNAs and in this way modulate cellular gene expression at the post-transcriptional level. Interestingly, the binding affinity of p19 varies considerably between different miRNAs, and the molecular determinants affecting this property have not yet been adequately characterized. Addressing this, we analyzed the binding of p19 to the miRNAs 162 and 168, which regulate the expression of the important RNA silencing constituents Dicer-like 1 (DCL1) and Argonaute 1 (AGO1), respectively. p19 binds miRNA162 with similar high affinity as siRNA, whereas the affinity for miRNA168 is significantly lower. We show that specific molecular features, such as mismatches and ‘G–U wobbles’ on the RNA side and defined amino acid residues on the VSR side, mediate this property. Our observations highlight the remarkable adaptation of VSR binding affinities to achieve differential effects on host miRNA activities. Moreover, they show that even minimal changes, i.e., a single base pair in a miRNA duplex, can have significant effects on the efficiency of the plant antiviral immune response. Full article
(This article belongs to the Special Issue Molecular Research on RNA Structure)
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12 pages, 1900 KiB  
Article
Structural Insights into Human Adenovirus Type 4 Virus-Associated RNA I
by Helen Bergquist, Raviteja Inturi, Rula Zain and Tanel Punga
Int. J. Mol. Sci. 2022, 23(6), 3103; https://doi.org/10.3390/ijms23063103 - 13 Mar 2022
Viewed by 1836
Abstract
RNA molecules can adopt specific RNA triplex structures to execute critical biological functions. Human adenoviruses (HAdVs) are abundant pathogens encoding the essential, noncoding virus-associated RNA I (VA RNAI). Here, we employ a triplex-specific probing assay, based on the intercalating and cleaving agent benzoquinoquinoxaline [...] Read more.
RNA molecules can adopt specific RNA triplex structures to execute critical biological functions. Human adenoviruses (HAdVs) are abundant pathogens encoding the essential, noncoding virus-associated RNA I (VA RNAI). Here, we employ a triplex-specific probing assay, based on the intercalating and cleaving agent benzoquinoquinoxaline 1, 10-phenanthroline (BQQ–OP), to unravel a potential RNA triplex formation in VA RNAI. The BQQ–OP cleavage of the pathogenic HAdV type 4 (HAdV-4) VA RNAI indicates that a potential triplex is formed involving the highly conserved stem 4 of the central domain and side stem 7. Further, the integrity of the HAdV-4 VA RNAI side stem 7 contributes to a potential triplex formation in vitro and virus growth in vivo. Collectively, we propose that the HAdV-4 VA RNAI can potentially form a biologically relevant triplex structure. Full article
(This article belongs to the Special Issue Molecular Research on RNA Structure)
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Review

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19 pages, 1193 KiB  
Review
Examples of Structural Motifs in Viral Genomes and Approaches for RNA Structure Characterization
by Maria Nalewaj and Marta Szabat
Int. J. Mol. Sci. 2022, 23(24), 15917; https://doi.org/10.3390/ijms232415917 - 14 Dec 2022
Cited by 1 | Viewed by 1447
Abstract
The relationship between conserved structural motifs and their biological function in the virus replication cycle is the interest of many researchers around the world. RNA structure is closely related to RNA function. Therefore, technological progress in high-throughput approaches for RNA structure analysis and [...] Read more.
The relationship between conserved structural motifs and their biological function in the virus replication cycle is the interest of many researchers around the world. RNA structure is closely related to RNA function. Therefore, technological progress in high-throughput approaches for RNA structure analysis and the development of new ones are very important. In this mini review, we discuss a few perspectives on the structural elements of viral genomes and some methods used for RNA structure prediction and characterization. Based on the recent literature, we describe several examples of studies concerning the viral genomes, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV). Herein, we emphasize that a better understanding of viral genome architecture allows for the discovery of the structure-function relationship, and as a result, the discovery of new potential antiviral therapeutics. Full article
(This article belongs to the Special Issue Molecular Research on RNA Structure)
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