Related Experiment Video
Updated: Jun 13, 2026
08:17
Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA
Published on: July 9, 2021
Real-time multidimensional NMR follows RNA folding with second resolution
Mi-Kyung Lee1, Maayan Gal, Lucio Frydman
1Department of Chemistry, University of Washington, Box 351700, Seattle WA 98195, USA.
Summary
Ultrafast NMR reveals the step-by-step folding of adenine riboswitches in real time. This study tracks RNA structural changes, offering insights into ligand-induced conformational transitions crucial for gene regulation.
Area of Science:
- Structural Biology
- Molecular Biophysics
- RNA Biology
Background:
- RNA conformational transitions are fundamental to biological function but poorly understood.
- Riboswitches are key regulatory elements whose function relies on ligand-induced structural changes.
- Real-time monitoring of these dynamic processes at nucleotide resolution is challenging.
Purpose of the Study:
- To investigate the real-time, nucleotide-resolved mechanism of adenine-induced riboswitch folding.
- To characterize the distinct structural intermediates and kinetic steps involved in riboswitch conformational changes.
- To demonstrate the utility of ultrafast multidimensional NMR for studying RNA dynamics.
Main Methods:
- Employed ultrafast multidimensional Nuclear Magnetic Resonance (NMR) spectroscopy.
- Monitored spectral changes at approximately 0.5 Hz to capture rapid folding events.
- Tracked adenine-induced folding of an adenine-sensing riboswitch in real time.
Main Results:
- Identified discrete steps in the ligand-induced folding pathway of the riboswitch.
- Observed the formation and progressive stabilization of long-range loop-loop interactions post-ligand binding.
- Characterized the complete folding process, culminating in a stable complex over 2-3 minutes.
Conclusions:
- Ultrafast multidimensional NMR enables the real-time observation of RNA conformational trajectories.
- The study elucidates a multi-step mechanism for adenine riboswitch folding initiated by ligand recognition.
- This methodology opens avenues for determining the structures of transient RNA folding intermediates.
Related Concept Videos
01:12Two-Dimensional (2D) NMR: Overview
The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse.
00:52¹H 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...
01:162D NMR: Overview of Homonuclear Correlation Techniques
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...
COSY90 is the standard two-dimensional (2D) COSY experiment that...
01:25Applications Of NMR In Biology
Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
The...
The...
01:02¹H NMR: Interpreting Distorted and Overlapping Signals
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
01:182D NMR: Overview of Heteronuclear Correlation Techniques
Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an X-nucleus, such as carbon-13 or nitrogen-15. This method is commonly used in nuclear magnetic resonance (NMR) spectroscopy to gain insights into complex chemical compounds' structural and compositional aspects. A typical heteronuclear correlation spectrum displays X-nucleus chemical shifts on one axis and a proton spectrum on the other axis.