Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

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...
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 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...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Understanding the role of short- and long-range intermolecular interactions in novel computational drug discovery.

Expert opinion on drug discovery·2025
Same author

Post-Transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates in <i>E. coli</i> Expressing a Helicase-Inactive DbpA Variant.

Biochemistry·2025
Same author

Assessment of the three-frequency pulse alternation method for simultaneously troposphere wind and aerosol profiling retrieval in a direct detection lidar.

Optics express·2025
Same author

Post-transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates in <i>E. coli</i> Expressing Helicase-Inactive DbpA Variant.

bioRxiv : the preprint server for biology·2025
Same author

Profiling of particulate matter transport flux based on dual-wavelength lidar and ensemble learning algorithm.

Optics express·2024
Same author

Evaluating sheep hemoglobins with MD simulations as an animal model for sickle cell disease.

Scientific reports·2024

Related Experiment Video

Updated: May 9, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes.

Rongzhong Li1, Heming W Ge, Samuel S Cho

  • 1Department of Physics, Wake Forest University , Winston-Salem, North Carolina 27106, United States.

The Journal of Physical Chemistry. B
|July 12, 2013
PubMed
Summary
This summary is machine-generated.

Bacterial transfer RNAs (tRNAs) fold via distinct mechanisms, influenced by sequence-dependent base-stacking. Simulations reveal these differences, explaining varied folding kinetics and identifying potential nonproductive folding intermediates.

More Related Videos

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
09:15

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Related Experiment Videos

Last Updated: May 9, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
09:15

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Bacterial transfer RNAs (tRNAs) exhibit structural similarity yet employ diverse folding mechanisms.
  • Understanding tRNA folding pathways is crucial for deciphering their biological functions.

Purpose of the Study:

  • To investigate the folding landscapes and mechanisms of bacterial tRNAs using molecular dynamics (MD) simulations.
  • To compare thermodynamic profiles and validate findings using both coarse-grained and atomistic simulations.
  • To correlate folding mechanisms with sequence-dependent base-stacking stabilities.

Main Methods:

  • Ion concentration-dependent coarse-grained TIS model MD simulations of E. coli tRNAs.
  • Atomistic empirical force field MD simulations for independent validation.
  • Comparison of base-to-base distances with empirical base-stacking free energies.
  • Projection of free energies onto tRNA secondary structural elements.

Main Results:

  • Distinct, parallel folding mechanisms were observed for different tRNAs, driven by sequence-specific base-stacking.
  • Coarse-grained and atomistic simulations yielded comparable results for base-stacking interactions.
  • A nonproductive folding intermediate involving the Ψ hairpin loop was identified in some cases.

Conclusions:

  • tRNA folding mechanisms are sequence-dependent, leading to distinct thermodynamic profiles.
  • The identified folding intermediates provide a potential explanation for observed fast and slow phases in tRNA folding kinetics.
  • MD simulations are effective tools for elucidating complex biomolecular folding pathways.