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Imperfections in Crystal Structure: Stoichiometric Point Defects01:26

Imperfections in Crystal Structure: Stoichiometric Point Defects

Schottky defects arise when some lattice points in a crystal, such as those in NaCl, remain unoccupied, creating lattice vacancies without disturbing the overall electrical neutrality of the crystal. This defect is common in ionic crystals where the positive and negative ions are similar in size, as seen in sodium chloride and cesium chloride. The presence of Schottky defects enables the crystal to conduct electricity to a small extent through an ionic mechanism. Electric fields cause nearby...

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A DNA-Based Binding Assay for the m6A-RNA Reader Proteins.

Rajiv Kumar Bedi1, Amedeo Caflisch1

  • 1Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Chembiochem : a European Journal of Chemical Biology
|March 21, 2026
PubMed
Summary

Researchers determined the crystal structure of the m6A-RNA reader YTHDC2, revealing a similar binding mode for both m6A-RNA and 6mA-DNA. They developed a robust DNA-based assay for high-throughput screening of modulators targeting these reader proteins.

Keywords:
6mA‐DNARNA binding proteinsepitranscriptomicsfluorescence polarizationm6A‐RNA

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Area of Science:

  • Epigenetics and Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • N6-methyladenosine (m6A) is a prevalent RNA modification crucial for gene regulation, with its dysregulation linked to various human diseases.
  • The role of N6-methyladenosine modifications in DNA (6mA) remains less understood and is an area of active research.
  • Understanding the interaction of m6A-RNA reader proteins with modified nucleic acids is vital for deciphering their biological functions.

Purpose of the Study:

  • To determine the first holo crystal structure of the m6A-RNA reader YTHDC2 bound to a modified DNA.
  • To compare the binding affinities and modes of m6A-RNA and 6mA-DNA with human reader proteins.
  • To develop a novel, high-throughput screening assay for identifying modulators of m6A-RNA reader proteins.

Main Methods:

  • Holo crystal structure determination of YTHDC2 complexed with a single-strand hexanucleotide GG(6mA)CTA-DNA at 1.6 Å resolution.
  • Comparative analysis using fluorescently labeled 6mA-ssDNA and m6A-RNA to assess binding affinities with five human m6A-RNA readers.
  • Development and validation of a fluorescence polarization (FP) binding assay utilizing a 6mA-containing ssDNA probe.

Main Results:

  • The crystal structure revealed an identical binding mode of 6mA-DNA to YTHDC2 as observed for m6A-RNA in other reader proteins.
  • Human m6A-RNA readers exhibited slightly stronger binding affinity for 6mA-modified DNA compared to m6A-RNA, with YTHDC2 showing a 30-fold increase.
  • A stable and robust DNA-based FP assay was successfully developed, demonstrating suitability for high-throughput screening.

Conclusions:

  • The structural and binding data suggest a conserved interaction mechanism between m6A-RNA readers and both m6A-RNA and 6mA-DNA.
  • The developed DNA-based FP assay offers a powerful and cost-efficient platform for discovering small-molecule modulators targeting m6A-RNA reader proteins.
  • This work facilitates further investigation into the roles of 6mA-DNA and m6A-RNA signaling in human health and disease.