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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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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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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RAG-Web: RNA structure prediction/design using RNA-As-Graphs.

Grace Meng1, Marva Tariq2, Swati Jain1

  • 1Department of Chemistry, New York University, New York, NY 10003, USA.

Bioinformatics (Oxford, England)
|August 3, 2019
PubMed
Summary
This summary is machine-generated.

We introduce RNA-As-Graphs (RAG) a novel webserver for RNA structure prediction and design. This tool utilizes graph theory to analyze RNA secondary structures and predict tertiary topologies for advanced RNA discovery.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • RNA structure prediction and design are crucial for understanding biological functions.
  • Existing methods often face challenges in accurately modeling complex RNA tertiary structures.
  • A graph-based approach offers a novel perspective for RNA analysis.

Purpose of the Study:

  • To present a new webserver, RAG-Web, for RNA structure prediction and design.
  • To introduce the RNA-As-Graphs (RAG) approach utilizing coarse-grained tree graphs.
  • To provide a user-friendly platform for researchers to explore RNA topology and sequence design.

Main Methods:

  • RNA secondary structures are represented as coarse-grained tree graphs.
  • The RAG Sampler module predicts tertiary topologies from secondary structures.
  • The RAG Builder module constructs 3D atomic models from predicted graphs.
  • The RAG Designer module designs RNA sequences for novel motifs.

Main Results:

  • The RAG-Web server integrates three modules for comprehensive RNA analysis.
  • The webserver facilitates the prediction of RNA tertiary structures.
  • The platform enables the design of RNA sequences folding onto specific topological motifs.
  • Results analysis and download options are provided for user convenience.

Conclusions:

  • RAG-Web offers a powerful and accessible tool for RNA structure prediction and design.
  • The RNA-As-Graphs approach advances RNA structure discovery through graph theory.
  • The webserver empowers researchers with novel capabilities in RNA motif design and analysis.