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Related Experiment Video

Updated: Jun 23, 2026

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

Structural probing techniques on natural aptamers.

Catherine A Wakeman1, Wade C Winkler

  • 1Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA.

Methods in Molecular Biology (Clifton, N.J.)
|April 21, 2009
PubMed
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Investigating RNA folding requires experimental methods beyond bioinformatics. This chapter details in-line probing for RNA secondary structure and backbone flexibility, and hydroxyl radical footprinting for RNA folding dynamics.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • RNA sequences fold hierarchically, forming secondary structures then tertiary contacts.
  • Bioinformatics tools struggle with accurate RNA secondary structure prediction.
  • Biochemical and biophysical techniques are essential for RNA structural analysis.

Purpose of the Study:

  • To outline a protocol for in-line probing to analyze RNA secondary structure and backbone flexibility.
  • To describe a protocol for hydroxyl radical footprinting to investigate RNA folding.

Main Methods:

  • In-line probing: Determines paired/unpaired nucleotides and backbone flexibility.
  • Hydroxyl radical footprinting: Assesses RNA structural dynamics and folding.
  • Experimental techniques complement bioinformatics for RNA structure elucidation.

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A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay
12:31

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Published on: February 28, 2015

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes
06:52

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Published on: November 1, 2019

Related Experiment Videos

Last Updated: Jun 23, 2026

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay
12:31

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Published on: February 28, 2015

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes
06:52

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Published on: November 1, 2019

Main Results:

  • In-line probing provides insights into RNA secondary structure and flexibility.
  • Hydroxyl radical footprinting reveals RNA folding pathways and dynamics.
  • These methods offer complementary data for comprehensive RNA structure analysis.

Conclusions:

  • Experimental probing methods are crucial for accurate RNA structural determination.
  • In-line probing and hydroxyl radical footprinting are valuable techniques for RNA research.
  • Combining multiple methods enhances understanding of complex RNA folding processes.