RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing

Ender, Anna; Stadler, Peter F.; Mörl, Mario; Findeiß, Sven

doi:10.1007/978-1-0716-2421-0_11

Cited by 2 publications

(1 citation statement)

References 52 publications

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“…RNAfold software was accessed from this link: http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold. cgi [44]. The conserved region of the MSA section was applied in this pipeline.…”

Section: Rnafold For Both Sirna and Mrna's 2d Structuresmentioning

confidence: 99%

A Computational Design of siRNA in SARS-CoV-2 Spike Glycoprotein Gene and Its Binding Capability toward mRNA

Parikesit

Ansori²,

Kharisma³

2022

Indones. J. Chem.

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COVID-19 pandemic has no immediate ending in sight, and any significant increasing cases were observed worldwide. Currently, there are only two main strategies for developing COVID-19 drugs that predominantly use a proteomics-based approach, which are drug repurposing and herbal medicine strategies. However, a third strategy has existed, called small interfering RNA or siRNA, which is based on the transcriptomics approach. In the case of SARS-CoV-2 infection, it is expected to perform by silencing the viral gene, which brings the surface glycoprotein (S) gene responsible for SARS-CoV-2 viral attachment to the ACE2 receptor on the human host cell. This third approach applies a molecular simulation method comprising data retrieval, multiple sequence alignment, phylogenetic tree depiction, 2D/3D structure prediction, and RNA-RNA molecular docking. The expected results are the prediction of 2D and 3D structures of both siRNA and mRNA silenced S genes along with a complex as the result of a docking method formed by those silenced genes. An Insilco chemical interaction study was performed in testing siRNA and mRNA complex’s stability with the confirmation result of a stable complex which is expected to be formed before mRNA reaches the ribosome for the translation process. Thus, siRNA from the S gene could be considered a candidate for the COVID-19 therapeutic agent.

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“…RNAfold software was accessed from this link: http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold. cgi [44]. The conserved region of the MSA section was applied in this pipeline.…”

Section: Rnafold For Both Sirna and Mrna's 2d Structuresmentioning

confidence: 99%

A Computational Design of siRNA in SARS-CoV-2 Spike Glycoprotein Gene and Its Binding Capability toward mRNA

Parikesit

Ansori²,

Kharisma³

2022

Indones. J. Chem.

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A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding

Mukherjee

Retwitzer

Hubbell

et al. 2023

Briefings in Bioinformatics

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Riboswitches are conserved structural ribonucleic acid (RNA) sensors that are mainly found to regulate a large number of genes/operons in bacteria. Presently, >50 bacterial riboswitch classes have been discovered, but only the thiamine pyrophosphate riboswitch class is detected in a few eukaryotes like fungi, plants and algae. One of the most important challenges in riboswitch research is to discover existing riboswitch classes in eukaryotes and to understand the evolution of bacterial riboswitches. However, traditional search methods for riboswitch detection have failed to detect eukaryotic riboswitches besides just one class and any distant structural homologs of riboswitches. We developed a novel approach based on inverse RNA folding that attempts to find sequences that match the shape of the target structure with minimal sequence conservation based on key nucleotides that interact directly with the ligand. Then, to support our matched candidates, we expanded the results into a covariance model representing similar sequences preserving the structure. Our method transforms a structure-based search into a sequence-based search that considers the conservation of secondary structure shape and ligand-binding residues. This method enables us to identify a potential structural candidate in fungi that could be the distant homolog of bacterial purine riboswitches. Further, phylogenomic analysis and evolutionary distribution of this structural candidate indicate that the most likely point of origin of this structural candidate in these organisms is associated with the loss of traditional purine riboswitches. The computational approach could be applicable to other domains and problems in RNA research.

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RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing

Cited by 2 publications

References 52 publications

A Computational Design of siRNA in SARS-CoV-2 Spike Glycoprotein Gene and Its Binding Capability toward mRNA

A Computational Design of siRNA in SARS-CoV-2 Spike Glycoprotein Gene and Its Binding Capability toward mRNA

A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding

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