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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...
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...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

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Related Experiment Video

Updated: Jun 15, 2026

Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters
10:52

Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters

Published on: May 29, 2026

Compact intermediates in RNA folding.

Sarah A Woodson1

  • 1T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA. swoodson@jhu.edu

Annual Review of Biophysics
|March 3, 2010
PubMed
Summary
This summary is machine-generated.

Large noncoding RNAs fold through compact, disordered intermediates that link secondary structure to tertiary folds. This process, influenced by RNA sequence and ions, dictates folding pathways and impacts biological functions like ligand binding.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • Large noncoding RNAs (ncRNAs) adopt complex three-dimensional structures essential for their biological functions.
  • RNA folding involves navigating complex energy landscapes, often through intermediate states.

Purpose of the Study:

  • To investigate the nature and role of compact, disordered intermediates in the folding pathways of large ncRNAs.
  • To understand how these intermediates couple secondary structure formation with tertiary fold assembly.

Main Methods:

  • The study likely employed biophysical techniques (e.g., spectroscopy, scattering) to probe RNA structure and dynamics.
  • Computational modeling may have been used to simulate folding pathways and intermediate states.

Main Results:

  • Large ncRNAs fold via compact, disordered intermediates that integrate secondary structure with nascent tertiary interactions.
  • The collapse transition, crucial for helical domain assembly, is sensitive to RNA sequence and counterion concentration.
  • These intermediates influence the specificity of folding pathways and the height of free energy barriers.

Conclusions:

  • Compact folding intermediates are key regulatory points in large ncRNA structural transitions.
  • These intermediates are critical for enabling specific ligand binding and RNA-protein interactions, highlighting their functional significance.