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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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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.
DNA Structure
DNA has a double-helix structure. The...
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...

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Related Experiment Video

Updated: May 30, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Understanding the errors of SHAPE-directed RNA structure modeling.

Wipapat Kladwang1, Christopher C VanLang, Pablo Cordero

  • 1Department of Biochemistry, Stanford University, Stanford, California 94305, USA.

Biochemistry
|August 17, 2011
PubMed
Summary
This summary is machine-generated.

Selective 2'-hydroxyl acylation by primer extension (SHAPE) chemical mapping shows RNA modeling errors. Benchmarking revealed significant false discovery and negative rates, indicating SHAPE data may lack sufficient information for accurate RNA structure prediction.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Bioinformatics

Background:

  • RNA structure prediction is crucial for understanding biological function.
  • Selective 2'-hydroxyl acylation by primer extension (SHAPE) is a powerful chemical mapping technique for RNA.
  • Recent advancements aim for near-zero error rates in SHAPE-based RNA secondary structure modeling.

Purpose of the Study:

  • To benchmark the accuracy of SHAPE-directed RNA structure modeling.
  • To evaluate the reliability of SHAPE data for predicting RNA helices.
  • To identify factors contributing to modeling errors and assess confidence in predictions.

Main Methods:

  • Benchmarking SHAPE-directed modeling against crystallographic data for six structured RNAs.
  • Systematic variation of data processing, normalization, and modeling parameters.
  • Nonparametric bootstrapping analysis to assess information content and confidence levels.

Main Results:

  • SHAPE-directed modeling yielded a 17% false negative rate and 21% false discovery rate across benchmark RNAs.
  • Modeling errors persisted despite extensive parameter variations.
  • Filtering deoxyinosine triphosphate data offered a modest improvement but did not eliminate errors.
  • Bootstrapping indicated insufficient SHAPE data information content for reliable helix prediction in many cases.

Conclusions:

  • SHAPE-directed RNA modeling is not always unambiguous and can contain significant errors.
  • Helix-by-helix confidence estimates are critical for interpreting SHAPE-based RNA structure models.
  • The reliability of SHAPE for RNA structure prediction depends on the information content of the specific RNA and data.