A Demethylation-Switchable Aptamer Design Enables Lag-Free Monitoring of m6A Demethylase FTO with Energy Self-Sufficient and Structurally Integrated Features

J Am Chem Soc. 2024 Dec 18;146(50):34638-34650. doi: 10.1021/jacs.4c12884. Epub 2024 Dec 4.

Abstract

Cellular context profiling of modification effector proteins is critical for an in-depth understanding of their biological roles in RNA N6-methyladenosine (m6A) modification regulation and function. However, challenges still remain due to the high context complexities, which call for a versatile toolbox for accurate live-cell monitoring of effectors. Here, we propose a demethylation-switchable aptamer sensor engineered with a site-specific m6A (DSA-m6A) for lag-free monitoring of the m6A demethylase FTO activity in living cells. As a proof of concept, a DNA aptamer against adenosine triphosphate (ATP) is selected to construct the DSA-m6A model, as the "universal energy currency" role of ATP could guarantee the equally fast and spontaneous conformation change of DSA-m6A sensor upon demethylation and ATP binding in living organisms, thus enabling sensitive monitoring of FTO activity with neither time delay nor recourse to extra supply of substances. This ATP-driven DSA-m6A design facilitates biomedical research, including live-cell imaging, inhibitor screening, single-cell tracking of dynamic FTO nuclear translocation upon starvation stimuli, FTO characterization in a biomimetic heterotypic three-dimensional (3D) multicellular spheroid model, as well as the first report on the in vivo imaging of FTO activity. This strategy provides a simple yet versatile toolbox for clinical diagnosis, drug discovery, therapeutic evaluation, and biological study of RNA demethylation.

MeSH terms

  • Adenosine Triphosphate* / chemistry
  • Adenosine Triphosphate* / metabolism
  • Adenosine* / analogs & derivatives
  • Adenosine* / chemistry
  • Adenosine* / metabolism
  • Alpha-Ketoglutarate-Dependent Dioxygenase FTO* / chemistry
  • Alpha-Ketoglutarate-Dependent Dioxygenase FTO* / metabolism
  • Aptamers, Nucleotide* / chemistry
  • Aptamers, Nucleotide* / metabolism
  • Demethylation*
  • Humans

Substances

  • Alpha-Ketoglutarate-Dependent Dioxygenase FTO
  • Aptamers, Nucleotide
  • FTO protein, human
  • Adenosine
  • Adenosine Triphosphate
  • N-methyladenosine