Diffusion modulation of DNA by toehold exchange

Thanapop Rodjanapanyakul, Fumi Takabatake, Keita Abe, Ibuki Kawamata, Shinichiro M. Nomura, Satoshi Murata

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experimental results show that the sequence-specific modulation of the diffusion coefficient is successfully achieved. The diffusion coefficient can be modulated up to sixfold by changing the concentration of the competitor. The specificity of the modulation is also verified under the coexistence of a set of DNA with noninteracting base sequences. With this mechanism, we are able to control the diffusion coefficient of individual DNA species by the concentration of another DNA species. This methodology introduces a programmability to a DNA-based reaction-diffusion system.

Original languageEnglish
Article number052617
JournalPhysical Review E
Issue number5
Publication statusPublished - 2018 May 31

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics


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