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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...

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

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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.

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Related Experiment Video

Updated: Jun 6, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

RNA tertiary structure and conformational dynamics revealed by BASH MaP.

Maxim Oleynikov¹, Samie R Jaffrey¹

¹Department of Pharmacology, Weill Medical College, Cornell University, New York, United States.

|December 3, 2024

Summary

We developed BASH MaP, a novel RNA tertiary structure analysis method, to uncover alternative RNA conformations. This approach reveals previously hidden RNA structures and dynamics, advancing our understanding of RNA function.

Keywords:

AKT2 DMS probing G-quadruplex chemical probing human molecular biophysics polyUG spinach structural biology

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Last Updated: Jun 6, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

RNA Secondary Structure Prediction Using High-throughput SHAPE

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Analyzing and Building Nucleic Acid Structures with 3DNA

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Published on: April 26, 2013

Area of Science:

Molecular Biology
Structural Biology
Biochemistry

Background:

RNA tertiary structures dictate diverse biological functions.
Predicting RNA tertiary conformations and identifying alternative structures remain significant challenges in molecular biology.

Purpose of the Study:

To develop and validate a novel method for identifying alternative RNA tertiary structures.
To investigate the conformational diversity and dynamics of RNA molecules, including G-quadruplexes and the Spinach aptamer.

Main Methods:

Development of BASH MaP (single-molecule dimethyl sulfate footprinting) to probe guanosine N7 accessibility.
Integration of BASH MaP with the DAGGER computational pipeline for analyzing alternative RNA structures.
Application of BASH MaP to study RNA G-quadruplexes in vitro and in cells, and the Spinach aptamer.

Main Results:

BASH MaP successfully identified diverse conformational states and dynamics of RNA G-quadruplexes.
Analysis of the Spinach aptamer revealed alternative tertiary conformations linked to its fluorescence states.
The study demonstrated the capability of BASH MaP to detect previously undetectable RNA tertiary structures.

Conclusions:

BASH MaP provides a powerful new approach for RNA structural analysis.
The method reveals alternative RNA tertiary structures and their functional implications.
This work enhances the understanding of RNA conformational heterogeneity and dynamics.