Designing a dnazyme logic gate system in conducting a three-step organic synthesis in a isothermal solution

Abstract

Multistep chemical syntheses are very common and useful in many industrial applications. A wide variety of consumer and industrial organic products are synthesized through these multistep synthesis reactions. However, many waste products are also generated as most of these multistep synthesis reactions do not proceed in 100% yield and the wastes are multiplied with every additional reaction step. Furthermore, it is very exhausting and difficult to monitor and control each reaction vessel at the same time; much manual efforts are needed to conduct long synthesis reactions. This will result in lower speed and efficiency of the reactions and hence reduce the productivity of the overall yield.

In comparison, biosynthesis metabolic pathways consisting of DNA or RNA templates have proven to be much more efficient than the traditional multistep synthesis reactions. Manipulation of reaction molecules is also much easier with biosynthesis pathways. With the recent development of DNA nanodevices such as DNA walkers, it is possible to carry out DNA-templated multistep synthesis reactions in a much efficient manner without any manual interventions to adjust the reaction conditions.

In this project, an Mg2+-dependent E6-type DNAzyme logic gate is designed in an attempt to carry out a DNA-templated three-step amine acylation reaction to synthesize a triamide product. This DNA-templated three-step synthesis reaction is carried out in an isothermal solution under room temperature and no external interventions are required. The reaction products are analyzed using liquid chromatography mass spectrometry (LC/MS).