Implementing digital computing with DNA-based switching circuits

Fei Wang,Chunhai Fan,Lihua Wang,Jiye Shi,Qian Li,Xueli Zhang,Hui Lv,Jiang Li

doi:10.1038/s41467-019-13980-y

Abstract

DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. Switching circuits that were originally proposed by Shannon in 1938 and nowadays widely used in telecommunication represent an alternative and efficient means to realize fast-speed and high-bandwidth communication. Here we develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. We further demonstrate the implementation of full-adder and square-rooting functions using DSCs, which only uses down to 1/4 DNA strands as compared with a dual-rail logic expression-based design. We expect that DSCs provide a design paradigm for digital computation with biomolecules.

Highlights

DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation
Limitations associated with logic gate circuits emerges, which hinders the scale-up for practical achievable computational tasks as follows. (i) Typical approaches to increase the scalability involves the combination of basic gates such as AND and OR5,13,20,21, which increases the use of gates22–26. (ii) Using uniform motif and implementing AND and OR gate with different threshold concentrations have shown high modularity and potential for constructing complex computing networks
Here we report a general strategy for modular design of DNA switching circuits (DSCs) to implement arbitrary digital DNA computing

Summary

Introduction

DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. We develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. SDR enables an enzyme-free implementation strategy to develop molecular circuits for arithmetical purpose[14,15], which offers high selection space of orthogonal molecules[16]. We develop an SDRbased strategy to experimentally realize DNA-based SCs (DSCs) for molecular digital computing. In a typical DSC, switches act as the sole basic functional element in a circuit, the molecular design is uniform, which allows high modularity, programmability, and scalability. We expect the increase of the computing speed with the reduced use of orthogonal molecules

Methods

Results

Conclusion