Multi-species consensus network of DNA strand displacement for concentration-to-strand translation

TL;DR

This paper introduces novel DNA-based chemical reaction networks that translate concentration levels into specific DNA strand species, enabling concentration measurement without fluorescence, with customizable features for various applications.

Contribution

The paper presents a new design of concentration translators using DNA strand displacement, combining consensus and conversion networks, with geometric analysis and computational comparison of different types.

Findings

CRNs operate effectively as concentration translators

Two types of translators demonstrate different switching behaviors

Translators can read concentration without fluorescence

Abstract

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.