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

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

1.3K
When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
1.3K
2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)01:19

2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)

1.1K
Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a heteronucleus. The HSQC experiment is similar to the heteronuclear correlation experiment (HETCOR) but is more sensitive. In the HSQC spectrum, the proton chemical shift is plotted on the horizontal F2 axis, while the 13C chemical shift is plotted on the vertical F1 axis. The corresponding proton and 13C spectra are also shown. The HSQC contour plot does...
1.1K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.3K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
1.3K
Protein Folding01:22

Protein Folding

124.3K
Overview
124.3K
2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

415
Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...
415

You might also read

Related Articles

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

Sort by
Same author

Structure and molecular function of the BCL7 proteins.

Biochemical Society transactions·2026
Same author

N-terminally acetylated Met11-Tau: a new pathological truncated Tau species with functional relevance in Alzheimer's disease.

Translational neurodegeneration·2026
Same author

Blocking RAN translation without altering repeat RNAs rescues <i>C9ORF72</i>-related ALS and FTD phenotypes.

Science (New York, N.Y.)·2026
Same author

FTLD-MAPT mutations and short 5'UTR Tau mRNAs increase Tau translation.

NAR molecular medicine·2025
Same author

Structure of the nucleosome-bound human BCL7A.

Nucleic acids research·2025
Same author

Argonaute 2 targets viral transcripts but not genomes of RNA viruses during antiviral RNA interference in Drosophila.

PLoS pathogens·2025

Related Experiment Video

Updated: Nov 10, 2025

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

15.7K

RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT.

Fatima Alghoul1, Gilbert Eriani1, Franck Martin2

  • 1Université de Strasbourg-Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN" CNRS UPR9002, Strasbourg, France.

Methods in Molecular Biology (Clifton, N.J.)
|April 1, 2021
PubMed
Summary

This study presents a chemical probing protocol to map RNA secondary structures using fluorescently labeled oligos. The method accurately identifies RNA folding, aiding in understanding RNA functions and designing novel RNA structures.

Keywords:
CMCTCapillary electrophoresisChemical probingDMSPrimer extensionQuSHAPERNA secondary structure

More Related Videos

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.7K
Synthesis and Structure Determination of &#181;-Conotoxin PIIIA Isomers with Different Disulfide Connectivities
11:44

Synthesis and Structure Determination of µ-Conotoxin PIIIA Isomers with Different Disulfide Connectivities

Published on: October 2, 2018

12.9K

Related Experiment Videos

Last Updated: Nov 10, 2025

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

15.7K
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.7K
Synthesis and Structure Determination of &#181;-Conotoxin PIIIA Isomers with Different Disulfide Connectivities
11:44

Synthesis and Structure Determination of µ-Conotoxin PIIIA Isomers with Different Disulfide Connectivities

Published on: October 2, 2018

12.9K

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • RNA secondary structures are crucial for diverse RNA functions.
  • Chemical probing utilizes modifying reagents to identify single-stranded RNA regions.
  • Understanding RNA structure is key to deciphering its biological roles.

Purpose of the Study:

  • To present a comprehensive in vitro protocol for identifying RNA secondary structures.
  • To demonstrate the utility of chemical probing with specific reagents.
  • To validate the method using a designed RNA structure.

Main Methods:

  • Chemical probing using Dimethyl Sulfate (DMS) and CMCT.
  • Mapping modifications via primer extension arrests.
  • Utilizing 5' fluorescently labeled primers for detection.

Main Results:

  • A detailed protocol for RNA secondary structure identification is provided.
  • The method successfully maps RNA nucleotide modifications.
  • Demonstrated efficiency using a designed RNA structure from Hox a3 mRNA.

Conclusions:

  • The developed protocol offers a robust method for characterizing RNA secondary structures.
  • This technique aids in the study of RNA folding and function.
  • The method is applicable to designing and analyzing novel RNA elements.