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Related Concept Videos

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 Structure01:19

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...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Fine-tuning structural RNA alignments in the twilight zone.

Andreas Bremges1, Stefanie Schirmer, Robert Giegerich

  • 1Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany.

BMC Bioinformatics
|May 4, 2010
PubMed
Summary

This study introduces planACstar, a novel method to improve RNA structural alignment in low-sequence identity regions. planACstar enhances the estimation of RNA secondary structure conservation when sequence similarity is below 55%.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Multiple sequence alignment and folding are standard for RNA structure conservation.
  • This method is effective at ~75% sequence similarity but struggles below 55% (twilight zone).
  • Low sequence identity obscures covariance signals, hindering reliable conservation estimation.

Purpose of the Study:

  • To develop a method for improving RNA secondary structure conservation in the twilight zone.
  • To enhance the accuracy of structural alignment for sequences with low sequence identity.

Main Methods:

  • Introduced planACstar, an iterative method combining alignment folding and pure structure alignment.
  • Refolds sequences individually based on a consensus structure, then aligns structures irrespective of sequence.
  • Derives an improved sequence alignment from the structure alignment for re-submission to alignment folding.

Main Results:

  • planACstar improves structural alignment in the twilight zone (30-55% sequence identity).
  • The method enhances structure conservation by an average of 10% using the structure conservation index.
  • Iteration can further improve conservation, though one step is often sufficient.

Conclusions:

  • planACstar effectively addresses limitations of traditional methods in low-sequence identity RNA alignment.
  • The developed method offers a significant improvement in estimating RNA secondary structure conservation.
  • Tools like ClustalW, RNAalifold, and RNAforester were employed to validate the findings.