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Related Concept Videos

RNA Structure01:19

RNA Structure

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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Stability01:53

RNA Stability

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...
RNA Stability01:53

RNA Stability

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...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...

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Related Experiment Videos

The influence of the local sequence environment on RNA loop structures.

Christian Schudoma1, Abdelhalim Larhlimi, Dirk Walther

  • 1Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany. schudoma@mpimp-golm.mpg.de

RNA (New York, N.Y.)
|June 2, 2011
PubMed
Summary

RNA loop structure is influenced by local sequence context, not just long-range base pairing. This finding suggests local RNA sequences significantly impact local loop formation, improving predictability.

Related Experiment Videos

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • RNA folding is a hierarchical process, with secondary structure forming before the 3D conformation.
  • The conformation of RNA loops is thought to be determined by backbone flexibility and global constraints.
  • The influence of local sequence context on RNA loop structure remains largely unexplored.

Purpose of the Study:

  • To investigate the extent to which local sequence context influences RNA loop backbone conformation.
  • To determine if local RNA loop structures are predictable from local sequence information alone.

Main Methods:

  • Utilized Random Forests machine learning algorithm.
  • Analyzed a nonredundant dataset of unpaired nucleotides from 97 Protein Data Bank (PDB) X-ray structures.
  • Predicted discrete backbone angle conformations (η/θ-pseudo-torsional space) using local sequence information.

Main Results:

  • Achieved prediction accuracies of up to 55% for RNA loop conformations using local sequence data.
  • Demonstrated significantly better-than-chance prediction accuracy (17%-25%).
  • Identified that bases near the central nucleotide have the strongest influence on its conformation.

Conclusions:

  • RNA loop structure is significantly influenced by local sequence context, in addition to long-range base-pairing interactions.
  • Local sequence information can predict aspects of local RNA loop structure.
  • Findings challenge the notion that RNA loop conformation is solely driven by global optimization constraints.