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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 Structure01:23

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 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...
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...

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Related Experiment Video

Updated: Jun 28, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Time-resolved RNA SHAPE chemistry.

Stefanie A Mortimer1, Kevin M Weeks

  • 1Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.

Journal of the American Chemical Society
|November 13, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces time-resolved SHAPE chemistry for RNA folding kinetics. It reveals that RNA tertiary structure forms in two steps, with long-range interactions limiting the overall folding rate.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) provides single-nucleotide resolution of RNA structure.
  • Existing SHAPE methods are suitable for equilibrium structures but limited for kinetic studies.
  • Understanding RNA folding dynamics is crucial for elucidating biological functions.

Purpose of the Study:

  • To develop time-resolved SHAPE chemistry for kinetic studies of RNA folding.
  • To investigate the step-wise formation of tertiary interactions during RNA folding.
  • To determine the rate-limiting steps in the folding of the RNase P specificity domain RNA.

Main Methods:

  • Extension of SHAPE chemistry using a benzoyl cyanide scaffold for rapid kinetic measurements (approx. 1 s snapshots).
  • Application of time-resolved SHAPE to monitor the folding of an RNase P specificity domain RNA.
  • Analysis of nucleotide flexibility and reactivity to infer structural changes over time.

Main Results:

  • Tertiary interactions in the RNase P RNA domain form in two distinct kinetic steps.
  • Local tertiary contacts form significantly faster than long-range interactions.
  • Overall folding is rate-limited by the simultaneous formation of distant interactions, not by the disruption of non-native structures.

Conclusions:

  • Time-resolved SHAPE chemistry enables facile kinetic studies of RNA folding at single-nucleotide resolution.
  • RNA folding involves distinct stages, with the formation of long-range tertiary contacts being a key rate-limiting step.
  • This methodology has broad potential for studying RNA structural dynamics and conformational changes in various biological contexts.