2021/02/21 by Toshiyuki Yamane, Yamane, Toshiyuki, E. Nakamura +3
Biochemistry, Genetics and Molecular Biology · Engineering · #Advanced biosensing and bioanalysis techniques #FOS: Biological sciences #Gene Regulatory Network Analysis #Molecular Communication and Nanonetworks #Molecular Networks (q-bio.MN)
paper · pdf · doi:10.48550/arxiv.2102.10613
openalex publication_date 2021/02/21 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/04
We propose novel chemical reaction networks to translate levels of concentration into unique DNA strand species, which we call concentration translators. Our design of the concentration translators is based on combination of two chemical reaction networks, consensus network and conversion network with any number of chemical species. We give geometric analysis of the proposed CRNs from the viewpoint of nonlinear dynamical systems and show that the CRNs can actually operate as translator. Our concentration translators exploit DNA strand displacement (DSD) reaction, which is known for a universal reaction that can implement arbitrary chemical reaction networks. We demonstrate two specific types of concentration translators (translator A and B) with different switching behavior and biochemical cost and compared their characteristics computationally. The proposed concentration translators have an advantage of being able to readout the concentration of targeted nucleic acid strand without any fluorescence-based techniques. These characteristics can be tailored according to requirements from applications, including dynamic range, sensitivity and implementation cost.