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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...
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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Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Structural insight into RNA hairpin folding intermediates.

Gregory R Bowman1, Xuhui Huang, Yuan Yao

  • 1Biophysics Program, Stanford University, Stanford, California 94305, USA.

Journal of the American Chemical Society
|July 3, 2008
PubMed
Summary

RNA hairpins, crucial for molecular function, may fold via multiple states. Simulations reveal intermediate structures, suggesting folding is not a simple reverse of unfolding, a common feature in biomolecular processes.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Chemistry

Background:

  • RNA hairpins are fundamental secondary structures in RNA molecules.
  • The folding mechanism of RNA hairpins (two-state vs. multi-state) remains under investigation.
  • Understanding hairpin folding is key to comprehending RNA structure-function relationships.

Purpose of the Study:

  • To investigate the folding pathway of a small tetraloop hairpin.
  • To determine if hairpin folding follows a two-state or multi-state model.
  • To identify potential intermediate structures during the folding process.

Main Methods:

  • Utilized a serial version of replica exchange molecular dynamics (REMD).
  • Employed a distributed computing environment for enhanced simulation capabilities.
  • Analyzed simulation trajectories to identify folding intermediates.

Main Results:

  • Identified several intermediate structures during hairpin folding.
  • These intermediates are consistent with existing experimental data.
  • Observed that the folding pathway is not a simple reversal of high-temperature unfolding.

Conclusions:

  • RNA hairpin folding likely proceeds through multiple states, involving transient intermediates.
  • The folding pathway may differ significantly from the unfolding pathway.
  • This complex folding mechanism could be a general characteristic of biomolecular folding processes.