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High-Affinity DNA Aptamers for Silicate Sensing in Cells.

Yanjun Wang1, Wenlu Meng1, Ruoyu Yao1

  • 1State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China.

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|April 8, 2026
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Summary

Researchers developed DNA aptamers to visualize silicon (Si) in living cells. These novel tools enable real-time mapping of intracellular silicates, advancing biological imaging and understanding of silicon's roles.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Bioimaging and Sensing
  • Materials Science

Background:

  • Silicon's biological roles are poorly understood due to limitations in visualizing it within living systems.
  • The complex and heterogeneous nature of biological silicates challenges existing imaging and analytical methods.
  • There is a critical need for tools to specifically detect and visualize silicon species in their native biological environments.

Purpose of the Study:

  • To develop novel molecular tools for the selective recognition and imaging of silicates in biological systems.
  • To create high-affinity DNA aptamers capable of binding to silicates with varying polymerization states.
  • To enable real-time visualization of intracellular silicon distribution and dynamics.

Main Methods:

  • Selection of single-stranded DNA aptamers using a three-dimensional silicified hydrogel screening system.
  • Validation of aptamer binding affinity and specificity using electrophoretic mobility shift assays (EMSA) and microscale thermophoresis (MST).
  • Engineering of fluorescent sensors based on selected aptamers for intracellular silicate imaging.
  • Molecular docking to elucidate silicate recognition mechanisms by aptamers.

Main Results:

  • Identification of high-affinity DNA aptamers with nanomolar dissociation constants for silicate recognition.
  • Demonstration of aptamer selectivity for silicates with distinct polymerization states.
  • Development of two fluorescent sensors capable of mapping intracellular silicate distributions with high specificity.
  • Successful real-time visualization of silicon in living cells using the engineered aptamer-based sensors.

Conclusions:

  • The developed aptamers represent the first reported molecules with selective recognition of silicates based on polymerization state.
  • The aptamer-based fluorescent sensors provide a powerful new tool for biological imaging of silicon.
  • This approach facilitates further investigation into the functional roles of biogenic silicon in living organisms.