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Related Concept Videos

Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Automated 3D RNA structure prediction using the RNAComposer method for riboswitches.

K J Purzycka1, M Popenda1, M Szachniuk2

  • 1Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland.

Methods in Enzymology
|March 2, 2015
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Summary

RNAComposer predicts RNA 3D structures from secondary structures. This method aids in understanding RNA functions and addresses the challenge of predicting large RNA molecules.

Keywords:
3D structureRNARNAComposerRiboswitchesStructure predictionc-di-GMP-II riboswitch

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Determining RNA three-dimensional (3D) structures is crucial for understanding their diverse functions.
  • Experimental methods like X-ray crystallography, NMR, and cryo-EM yield limited RNA 3D structures compared to proteins.
  • This scarcity drives the need for accurate computational RNA 3D structure prediction methods.

Purpose of the Study:

  • To present RNAComposer, an automated method and server for predicting RNA 3D structures from secondary structure information.
  • To discuss the scope and limitations of RNAComposer, particularly for predicting riboswitch 3D structures.
  • To demonstrate the utility of RNAComposer using the cyclic di-GMP-II riboswitch as a case study.

Main Methods:

  • RNAComposer utilizes secondary structure information for automated 3D structure prediction.
  • Supporting servers RNA FRABASE and RNApdbee facilitate secondary and 3D structure analysis.
  • RNAlyzer provides tools for analyzing and visualizing the quality of predicted RNA 3D models.

Main Results:

  • RNAComposer successfully predicted the 3D structure of the cyclic di-GMP-II riboswitch from Clostridium acetobutylicum (PDB ID 3Q3Z).
  • The method was applied to predict structures of related riboswitches from other bacterial species with unknown structures.
  • The study highlights the potential of RNAComposer for predicting structures of functional RNA elements like riboswitches.

Conclusions:

  • RNAComposer offers a valuable tool for automated RNA 3D structure prediction, addressing a significant challenge in structural biology.
  • The method, along with its supporting servers, enhances the ability to study RNA structures and functions computationally.
  • RNAComposer shows promise for predicting the structures of biologically relevant RNA molecules, including riboswitches.