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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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RNA Structure01:23

RNA Structure

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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
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RNA Structure01:23

RNA Structure

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RNA Structure01:19

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Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.

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Dynamics of tRNA at different levels of hydration.

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Time-resolved hydroxyl radical footprinting of RNA with X-rays.

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Related Experiment Video

Updated: Jul 5, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Probing RNA folding pathways by RNA fingerprinting.

S A Woodson1

  • 1Johns Hopkins University, Baltimore, Maryland, USA.

Current Protocols in Nucleic Acid Chemistry
|April 23, 2008
PubMed
Summary

Native polyacrylamide gel electrophoresis (native PAGE) effectively separates RNA folding conformers. This method enables studying RNA dynamics and catalytic activity, overcoming limitations of solution-based techniques.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Studying RNA folding and unfolding dynamics is crucial for understanding RNA function.
  • Solution-based methods often struggle to capture transient RNA conformers due to rapid exchange rates.
  • Characterizing RNA-protein complexes requires methods that preserve structural integrity.

Purpose of the Study:

  • To provide protocols for distinguishing RNA folding and unfolding conformers using native polyacrylamide gel electrophoresis (native PAGE).
  • To enable the study of RNA conformers with exchange periods in the minutes or seconds range.
  • To facilitate the investigation of catalytic activity of separated RNA conformers and RNA-protein complexes.

Main Methods:

  • Utilizing native polyacrylamide gel electrophoresis (native PAGE) for RNA conformational analysis.

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  • Separating and immobilizing distinct RNA conformers within the gel matrix.
  • Assessing catalytic activity of immobilized conformers, with or without elution.

    • Main Results:

    • Native PAGE successfully distinguishes between folding and unfolding RNA conformers.
    • The method is applicable to RNA conformers with rapid exchange kinetics.
    • Catalytic activities of separated conformers can be reliably assessed.

    Conclusions:

    • Native PAGE is a powerful technique for analyzing dynamic RNA structures.
    • This protocol allows for detailed investigation of RNA folding pathways and functions.
    • The method is versatile and applicable to various catalytic RNAs and RNA-protein complexes.