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RNA Function and Structure
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RNA Function and Structure

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 (20 April 2025) | Viewed by 6187

Special Issue Editor

Dr. Anna Wacker

E-Mail Website
Guest Editor
Schwalbe Lab, Institute for Organic Chemistry, Goethe University Frankfurt, Frankfurt, Germany
Interests: riboswitch RNA; RNA structural dynamics; variations of canonical RNA motifs; NMR spectroscopy of non-static RNA

Special Issue Information

Dear Colleagues,

As of the current moment, with the award of the Nobel Prize to Katalin Kariko, the realization has reached the general public that RNA provides valuable and diverse functions that we can and must harness. In order to build up a similar repertoire of tools and systems that have long existed for proteins, we need fundamental knowledge of the structural principles underlying the function of RNA. This Special Issue is dedicated to research on precisely this connection between RNA function and its structure. Both research articles and review papers are welcomed in the Special Issue.

Dr. Anna Wacker
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.

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Keywords

  • RNA architecture
  • molecular motions
  • structural dynamics
  • NMR spectroscopy
  • RNA–RNA interaction
  • RNA-binding proteins
  • RNA–ligand complex
  • RNA recognition
  • RNA modifications
  • RNA targeting

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Published Papers (2 papers)

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Research

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11 pages, 1326 KiB  
Article
Integrating PLOR and SPAAC Click Chemistry for Efficient Site-Specific Fluorescent Labeling of RNA
by Yanyan Xue, Xiao Si, Daxu Yin, Shengzhe Zhang and Hua Dai
Int. J. Mol. Sci. 2025, 26(6), 2601; https://doi.org/10.3390/ijms26062601 - 13 Mar 2025
Viewed by 747
Abstract
Precisely fluorescently labeling specific nucleotide sites of RNA is critical for gaining insights into the structure and function of RNA through multiple fluorescence detection techniques. The position-selective labeling of RNA (PLOR) method provides a promising strategy to achieve this, wherein the fluorophore-modified NTPs [...] Read more.
Precisely fluorescently labeling specific nucleotide sites of RNA is critical for gaining insights into the structure and function of RNA through multiple fluorescence detection techniques. The position-selective labeling of RNA (PLOR) method provides a promising strategy to achieve this, wherein the fluorophore-modified NTPs can be co-transcriptionally introduced to specific sites of nascent RNA by using T7 RNA polymerase (T7 RNAP). However, due to steric hindrance limitations, the efficiency of T7 RNAP in recognizing and incorporating large fluorophore-modified NTPs into RNA is far from satisfactory. To overcome this challenge, in this work, we developed an efficient PLOR variant (ePLOR) for the site-specific fluorescent labeling of RNA by integrating PLOR with a post-transcriptional SPAAC (strain-promoted azido-alkyne cycloaddition) click chemistry reaction. The efficiency of the SPAAC reaction occurring on RNA is nearly 100%. Consequently, ePLOR enables the precise fluorescent labeling of designated sites across various structural regions of SAM-VI riboswitch and adenine riboswitch RNA, with labeling and synthesis efficiencies that are 2–2.5 times higher than those of PLOR. The strategy developed in this work can be used for the efficient synthesis of a broader spectrum of long-strand RNAs with site-specific fluorescent labeling and greatly facilitate the detection of the structure and function of these RNAs. Full article
(This article belongs to the Special Issue RNA Function and Structure)
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Review

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16 pages, 1124 KiB  
Review
An Overview of Current Detection Methods for RNA Methylation
by Buket Sağlam and Bünyamin Akgül
Int. J. Mol. Sci. 2024, 25(6), 3098; https://doi.org/10.3390/ijms25063098 - 7 Mar 2024
Cited by 16 | Viewed by 4693
Abstract
Epitranscriptomic mechanisms, which constitute an important layer in post-transcriptional gene regulation, are involved in numerous cellular processes under health and disease such as stem cell development or cancer. Among various such mechanisms, RNA methylation is considered to have vital roles in eukaryotes primarily [...] Read more.
Epitranscriptomic mechanisms, which constitute an important layer in post-transcriptional gene regulation, are involved in numerous cellular processes under health and disease such as stem cell development or cancer. Among various such mechanisms, RNA methylation is considered to have vital roles in eukaryotes primarily due to its dynamic and reversible nature. There are numerous RNA methylations that include, but are not limited to, 2’-O-dimethyladenosine (m6Am), N7-methylguanosine (m7G), N6-methyladenosine (m6A) and N1-methyladenosine (m1A). These biochemical modifications modulate the fate of RNA by affecting the processes such as translation, target site determination, RNA processing, polyadenylation, splicing, structure, editing and stability. Thus, it is highly important to quantitatively measure the changes in RNA methylation marks to gain insight into cellular processes under health and disease. Although there are complicating challenges in identifying certain methylation marks genome wide, various methods have been developed recently to facilitate the quantitative measurement of methylated RNAs. To this end, the detection methods for RNA methylation can be classified in five categories such as antibody-based, digestion-based, ligation-based, hybridization-based or direct RNA-based methods. In this review, we have aimed to summarize our current understanding of the detection methods for RNA methylation, highlighting their advantages and disadvantages, along with the current challenges in the field. Full article
(This article belongs to the Special Issue RNA Function and Structure)
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