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Diffusion is the passive movement of substances down their concentration gradients—requiring no expenditure of cellular energy. Substances, such as molecules or ions, diffuse from an area of high concentration to an area of low concentration in the cytosol or across membranes. Eventually, the concentration will even out, with the substance moving randomly but causing no net change in concentration. Such a state is called dynamic equilibrium, which is essential for maintaining overall...
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Diffusion is a type of passive transport. In passive transport, a substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across the space. For example, take the diffusion of substances through the air. When someone opens a perfume bottle in a room filled with people, the perfume is at its highest concentration in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the...
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Related Experiment Video

Updated: Feb 8, 2026

Design to Implementation Study for Development and Patient Validation of Paper-Based Toehold Switch Diagnostics
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Diffusion modulation of DNA by toehold exchange.

Thanapop Rodjanapanyakul1, Fumi Takabatake2, Keita Abe1

  • 1Department of Robotics, Tohoku University, Sendai 980-8579, Japan.

Physical Review. E
|June 17, 2018
PubMed
Summary

We developed a DNA-based method to control diffusion speed in polymer solutions. By adjusting competitor DNA concentration, we can programmatically alter the movement of target DNA sequences up to sixfold.

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Area of Science:

  • Biochemistry
  • Materials Science
  • Molecular Biology

Background:

  • Controlling molecular diffusion is crucial for DNA-based reaction-diffusion systems.
  • Existing methods lack precise, sequence-specific control over diffusion dynamics.

Purpose of the Study:

  • To introduce a programmable method for modulating the diffusion speed of specific DNA molecules.
  • To demonstrate sequence-specific control over DNA diffusion using toehold exchange.

Main Methods:

  • Utilizing a polymer solution with anchored diffusion-suppressing DNA.
  • Modulating solute DNA-polymer interactions via competitor DNA and toehold exchange.
  • Experimentally measuring diffusion coefficients under varying competitor concentrations.

Main Results:

  • Achieved sequence-specific modulation of DNA diffusion coefficients.
  • Demonstrated up to a sixfold change in diffusion speed by altering competitor DNA concentration.
  • Verified specificity even with non-interacting DNA sequences present.

Conclusions:

  • The proposed toehold exchange mechanism enables programmable control over individual DNA species' diffusion.
  • This methodology enhances the programmability of DNA-based reaction-diffusion systems.