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Updated: Jun 28, 2026
06:02
Determining the Thermodynamic and Kinetic Association of a DNA Aptamer and Tetracycline Using Isothermal Titration Calorimetry
Published on: August 23, 2022
Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial
Hong Xiao1, Thomas E Edwards, Adrian R Ferré-D'Amaré
1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.
Chemistry & Biology
|October 23, 2008
Summary
The tetracycline aptamer binds antibiotics with high affinity. Its complex structure, revealed by X-ray crystallography, explains its function in gene regulation.
Area of Science:
- Molecular Biology
- Structural Biology
- RNA Therapeutics
Background:
- The tetracycline aptamer is an artificial RNA with exceptionally high affinity for tetracycline (Kd ~0.8 nM).
- It is one of the few aptamers capable of modulating gene expression in vivo.
- Understanding its structure is key to its application in gene regulation.
Purpose of the Study:
- To elucidate the 3D structure of the tetracycline aptamer.
- To understand the mechanism of tetracycline binding.
- To compare the aptamer's structure to natural riboswitches.
Main Methods:
- X-ray crystallography at 2.2 Å resolution to determine the aptamer's cocrystal structure.
- Integration of biochemical and biophysical data.
Main Results:
- The aptamer forms a pseudoknot-like fold via tertiary interactions.
- Tetracycline binds within a magnesium ion chelate at the interface of an 11-nucleotide loop and an irregular helix.
- The aptamer exhibits a complex three-helix junction, h-shaped architecture.
Conclusions:
- The aptamer's structure reveals localized folding upon tetracycline binding.
- Its complex architecture is similar to natural riboswitches, suggesting shared structural principles.
- This structural insight facilitates the development of RNA-based gene regulatory tools.
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