Implementing digital computing with DNA-based switching circuits

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 fastspeed 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 expressionbased design. We expect that DSCs provide a design paradigm for digital computation with biomolecules.

Propelling DNA Computing with Materials’ Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio‐Applications

“…Recently, Fan's group combined TMSD with DNA switching circuits (DSCs) together and realized a set of DSCs-based digital computing functions (such as full-adding), Figure 4E. [43] They demonstrated that arbitrary Boolean functions can be implemented by DSCs with high computing speed, thus providing an inspiring paradigm for biomolecular computing. All above works depend only on the innovation of DNA hybridization technology, the TMSD reaction and fluorophorelabeled DNAs, not on functional materials, which act the leading and enlightening role in DNA computing.…”

“…[42] Copyright 2011, American Chemical Society; E) Switching circuit-based DNA logic system, Reproduced with permission. [43] Copyright 2020, Springer Nature.…”

Supra-molecular agents running tasks intelligently (SMARTI): recent developments in molecular logic-based computation

“…Molecular implementations of this should be possible in the near future for the case of electronic conduction output of photochromic units under various stimulations. 101,102,246 Section 7 mentioned related 212 This fundamental idea is now realized with DNA devices 247 based on toehold-mediated strand exchange. 135 Fig.…”

Programming DNA‐Based Systems through Effective Molarity Enforced by Biomolecular Confinement

“…The predictable hybridization between complementary base pairs that underlies the self‐assembly of DNA lays the chemical foundation for engineering highly structured materials, dynamic nanodevices and complex reaction networks for molecular computation . Functional DNA nanotechnology has greatly benefited from the extensive use of programmable strand displacement reactions upholding the design of stimuli‐responsive DNA switches, enzyme‐free catalytic systems, or molecular computers .…”