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

Intermolecular vs Intramolecular Forces03:00

Intermolecular vs Intramolecular Forces

Intermolecular forces (IMF) are electrostatic attractions arising from charge-charge interactions between molecules. The strength of the intermolecular force is influenced by the distance of separation between molecules. The forces significantly affect the interactions in solids and liquids, where the molecules are close together. In gases, IMFs become important only under high-pressure conditions (due to the proximity of gas molecules). Intermolecular forces dictate the physical properties of...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Radical Reactivity: Intramolecular vs Intermolecular01:33

Radical Reactivity: Intramolecular vs Intermolecular

Radical reactions can occur either intermolecularly or intramolecularly. In an intermolecular radical reaction, a nucleophilic radical adds to an electrophilic alkene or vice versa. In such reactions, the radical and generally the alkene, which is also called the radical trap, are two different molecules. Additionally, for such intermolecular reactions to occur, the radical trap must be active, present in an excess concentration, and the radical starting material must have a weak carbon–halogen...
Atomic Nuclei: Types of Nuclear Relaxation01:28

Atomic Nuclei: Types of Nuclear Relaxation

Nuclear relaxation restores the equilibrium population imbalance and can occur via spin–lattice or spin–spin mechanisms, which are first-order exponential decay processes.
In spin–lattice or longitudinal relaxation, the excited spins exchange energy with the surrounding lattice as they return to the lower energy level. Among several mechanisms that contribute to spin–lattice relaxation, magnetic dipolar interactions are significant. Here, the excited nucleus transfers energy to a nearby...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

You might also read

Related Articles

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

Sort by
Same author

Sex-specific regulation of angiogenin in Alzheimer's disease.

Molecular psychiatry·2026
Same author

ModiCal: A Targeted Calibration Workflow for Site-Specific m<sup>5</sup>C Validation by Nanopore Direct RNA Sequencing.

ACS chemical biology·2026
Same author

Real-time transcriptomic profiling in distinct experimental conditions.

eLife·2026
Same author

Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read nanopore sequencing.

Nature communications·2026
Same author

Complementary DNA oligonucleotide direct in-gel quantification (cDINGQ) for precise tRNA fragment analysis.

RNA (New York, N.Y.)·2026
Same author

The two-step purification method ViREn identifies a single NSUN6-mediated 5-methylcytosine modification promoting dengue virus RNA genome turnover.

Nucleic acids research·2026

Related Experiment Video

Updated: Jun 30, 2026

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
09:25

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins

Published on: November 1, 2024

RNA intramolecular dynamics by single-molecule FRET.

Martin Hengesbach1, Andrei Kobitski, Felix Voigts-Hoffmann

  • 1Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany.

Current Protocols in Nucleic Acid Chemistry
|September 27, 2008
PubMed
Summary

This study details synthesizing and investigating RNA molecules using fluorescence resonance energy transfer (FRET). It provides methods for labeling RNA with dyes and analyzing folding dynamics via single-molecule spectroscopy.

More Related Videos

Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
10:23

Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules

Published on: April 25, 2025

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

Related Experiment Videos

Last Updated: Jun 30, 2026

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
09:25

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins

Published on: November 1, 2024

Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
10:23

Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules

Published on: April 25, 2025

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

Area of Science:

  • Biochemistry
  • Biophysics
  • Chemical Biology

Background:

  • Single-molecule fluorescence resonance energy transfer (FRET) is crucial for studying RNA folding dynamics and thermodynamics.
  • Investigating RNA folding requires expertise spanning chemistry, biochemistry, and physics.

Purpose of the Study:

  • To provide detailed protocols for synthesizing RNA molecules labeled with two FRET-interacting fluorescent dyes.
  • To outline methods for investigating these labeled RNA molecules using single-molecule fluorescence spectroscopy.

Main Methods:

  • Synthesis of RNA molecules with specific labeling of two fluorescent dyes.
  • Application of fluorescence resonance energy transfer (FRET) for molecular interaction studies.
  • Utilizing single-molecule fluorescence spectroscopy for dynamic and thermodynamic analysis.

Main Results:

  • Successful synthesis of dual-labeled RNA molecules suitable for FRET analysis.
  • Demonstration of FRET-based investigation of RNA folding processes.
  • Acquisition of data on dynamic and thermodynamic properties of RNA folding.

Conclusions:

  • The described methods enable detailed investigation of RNA folding at the single-molecule level.
  • This interdisciplinary approach enhances understanding of RNA conformational dynamics.
  • The protocols facilitate reproducible FRET-based studies in RNA research.