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Related Experiment Video

Updated: May 6, 2026

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

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Published on: January 7, 2017

Measuring Aptamer Folding Energy Using a Molecular Clamp.

Hao Qu¹, Qihui Ma¹, Lu Wang¹

¹School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.

Journal of the American Chemical Society

|June 4, 2020

Summary

Researchers developed a simple method to measure aptamer folding energy, a key factor in aptamer stability and function. This technique uses DNA molecular clamps and gel electrophoresis to determine folding energy, aiding aptamer research.

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Last Updated: May 6, 2026

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Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

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Area of Science:

Biophysics
Molecular Biology
Biochemistry

Background:

Aptamer folding energy (ΔGfold) is crucial for understanding aptamer stability and function.
Experimental measurement of aptamer folding energy is challenging due to the lack of general techniques.

Purpose of the Study:

To present a straightforward and generalizable method for measuring aptamer folding energy.
To provide a new tool for characterizing aptamer stability and function.

Main Methods:

Utilizing a double-stranded DNA molecular clamp coupled to aptamer ends to stretch the aptamer under equilibrium conditions.
Employing time-lapse gel electrophoresis to measure the total internal energy of stressed DNA molecules.
Comparing folding and unfolding behaviors of aptamer-containing and unstructured DNA molecules to derive aptamer folding energy.

Main Results:

Successfully measured the folding energy of the HD22 thrombin aptamer as 10.40 kJ/mol, aligning with existing predictions.
Determined the folding energy of a simple hairpin structure to be 9.05 kJ/mol, closely matching computational predictions (9.24 kJ/mol).

Conclusions:

The developed strategy offers an accessible and generalizable approach for measuring folding energy in various aptamers.
This method facilitates a more accurate characterization of aptamer stability and function.