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siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
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RNA Structure

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Related Experiment Video

Updated: May 16, 2026

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

On topological indices for small RNA graphs.

Alexander Churkin1, Idan Gabdank, Danny Barash

  • 1Department of Computer Science, Ben-Gurion University, 84105 Beer-Sheva, Israel.

Computational Biology and Chemistry
|November 14, 2012
PubMed
Summary

This study introduces a new method to analyze small RNA graphs using topological indices like the Szeged index. This approach helps quantify RNA topology by considering all Laplacian eigenvalues, advancing RNA structure analysis.

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Last Updated: May 16, 2026

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • RNA secondary structures can be represented by graphs.
  • Topological indices are useful for distinguishing RNA structures.
  • Existing methods are insufficient for analyzing small RNA full graphs.

Purpose of the Study:

  • To develop a meaningful topological index for small RNA full graphs.
  • To adapt existing topological indices for cyclic RNA graphs.
  • To quantify the topology of small RNA graphs using Laplacian eigenvalues.

Main Methods:

  • Representing small RNA secondary structures as full graphs.
  • Applying elementary cuts to analyze cyclic RNA graphs.
  • Calculating the Szeged index for small RNA graphs.

Main Results:

  • Demonstrated the calculation of the Szeged index for small RNA graphs.
  • Showed that elementary cuts enable topological analysis of cyclic RNA graphs.
  • Proposed a method considering all Laplacian eigenvalues for RNA topology quantification.

Conclusions:

  • The Szeged index, calculated via elementary cuts, is suitable for small RNA graph analysis.
  • This method provides a way to quantify RNA topology using all Laplacian eigenvalues.
  • The approach offers potential for distinguishing and analyzing diverse small RNA structures.