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Updated: Sep 11, 2025

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Structural basis and affinity improvement for an ATP-binding DNA aptamer.

Yan Jiang1,2, Yuchao Zhang2, Liqi Wan2

  • 1Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo and Biosensing, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.

Proceedings of the National Academy of Sciences of the United States of America
|August 14, 2025
PubMed
Summary

Researchers elucidated the structure and binding mechanism of a DNA aptamer for adenosine triphosphate (ATP). Modifications improved ATP binding affinity, enabling new DNA-based molecular tools.

Keywords:
DNA aptamerDNA structurehigh-resolution structuresolution NMR

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • DNA aptamers offer high affinity for small molecules, revolutionizing biosensing and bioimaging.
  • The DNA aptamer 1301b shows high potency for adenosine triphosphate (ATP) binding (Kd ~2.7 µM), but its structural basis is unknown.

Purpose of the Study:

  • To determine the structural basis and recognition mechanism of the 1301b DNA aptamer for ATP.
  • To engineer an improved DNA aptamer with enhanced ATP binding affinity.

Main Methods:

  • Solution NMR spectroscopy to determine the tertiary structure of a shortened aptamer (1301b_v1) complexed with ATP.
  • Structure-guided design incorporating 2'-O-methyl modifications to enhance binding affinity.

Main Results:

  • The 1301b_v1-ATP complex adopts an 'L' shape with ATP binding in a pocket formed by internal loops.
  • ATP binding involves hydrogen bonding with G14 and pi-stacking interactions with T8·A28 and G9.
  • An adaptive binding mechanism was observed, with the aptamer transitioning to a stable tertiary structure upon ATP binding.
  • The modified aptamer 9/10/16^OMe exhibited a significantly improved ATP binding affinity (Kd ~0.7 µM).

Conclusions:

  • The study reveals the detailed structural basis and adaptive binding mechanism of a potent DNA aptamer for ATP.
  • Structure-function insights enabled the development of an enhanced DNA aptamer with higher affinity for ATP.
  • These findings highlight the potential of DNA aptamers as sophisticated molecular tools for various applications.