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Related Concept Videos

RNA Structure01:23

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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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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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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Introduction to RNA secondary structure comparison.

Stefanie Schirmer1, Yann Ponty, Robert Giegerich

  • 1Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Universite de Montre al, Montre al, QC, Canada.

Methods in Molecular Biology (Clifton, N.J.)
|March 19, 2014
PubMed
Summary

This chapter reviews RNA secondary structure comparison methods, focusing on representations and techniques like base pair distances and tree edit models for structures without pseudo-knots. Comparing RNA structures with pseudo-knots remains an active research area.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA secondary structure comparison is crucial for understanding RNA function.
  • Numerous methods exist, with ongoing development in the field.
  • Pseudo-knots present unique challenges in RNA structure analysis.

Purpose of the Study:

  • To provide a comprehensive overview of RNA secondary structure comparison methods.
  • To discuss suitable structure representations for comparison.
  • To review existing tools and literature for RNA structure analysis.

Main Methods:

  • Evaluation of structure representations for comparative analysis.
  • Analysis of base pair distances for same-sequence structure comparison.
  • Application of tree edit model variants for different-sequence structure comparison (excluding pseudo-knots).

Main Results:

  • Commonly used methods for RNA secondary structure comparison (without pseudo-knots) are detailed.
  • Base pair distances and tree edit models are presented as effective comparison metrics.
  • Existing tools and relevant literature are identified.

Conclusions:

  • The chapter offers a structured approach to RNA secondary structure comparison.
  • Methods for comparing structures without pseudo-knots are well-established.
  • RNA secondary structure comparison with pseudo-knots is an open research problem.