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RNA Structure01:19

RNA Structure

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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 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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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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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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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Predicting RNA structure: advances and limitations.

Ivo L Hofacker1, Ronny Lorenz

  • 1Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.

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|October 19, 2013
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Summary
This summary is machine-generated.

This chapter details using the ViennaRNA Package for RNA secondary structure prediction and folding kinetics analysis. It covers minimum free energy, suboptimal structures, base pairing probabilities, and Markov process simulations for RNA folding.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Molecular biology

Background:

  • RNA secondary structures play crucial roles in gene regulation and molecular mechanisms.
  • Predicting these structures computationally is essential for understanding RNA function.
  • The ViennaRNA Package is a widely adopted software suite for RNA structure analysis.

Purpose of the Study:

  • To provide a guide on utilizing the ViennaRNA Package for common RNA secondary structure prediction tasks.
  • To introduce recent computational methods for assessing RNA folding kinetics.
  • To enable researchers to visualize and interpret RNA structure predictions and folding dynamics.

Main Methods:

  • Prediction of minimum free-energy (MFE) secondary structures.
  • Calculation of suboptimal structures and base pairing probabilities.
  • Generation of secondary structure plots with reliability annotations.
  • Assessment of RNA folding kinetics using 2D energy landscape projections.
  • Identification of local minima and energy barriers in folding pathways.
  • Simulation of RNA folding dynamics as a Markov process.

Main Results:

  • Demonstration of practical applications of ViennaRNA Package tools for structure prediction.
  • Explanation of how to interpret reliability annotations on secondary structure plots.
  • Presentation of novel approaches for analyzing RNA folding pathways and kinetics.
  • Insights into the dynamics of RNA folding through computational simulations.

Conclusions:

  • The ViennaRNA Package offers a comprehensive suite of tools for RNA secondary structure prediction and analysis.
  • Advanced methods are available for investigating RNA folding kinetics and dynamics.
  • This guide empowers researchers to effectively use computational tools for RNA structure and folding studies.