High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis

Abstract

Powerful information processing and ubiquitous computing are crucial for all machines and living organisms. The Watson-Crick base-pairing principle endows DNA with excellent recognition and assembly abilities, which facilitates the design of DNA computers for achieving intelligent systems. However, current DNA computational systems are always constrained by poor integration efficiency, complicated device structures or limited computational functions. Here, we show a DNA arithmetic logic unit (ALU) consisting of elemental DNA logic gates using polymerase-mediated strand displacement. The use of an enzyme resulted in highly efficient logic gates suitable for multiple and cascaded computation. Based on our basic single-rail DNA configuration, additional combined logic gates (e.g., a full adder and a 4:1 multiplexer) have been constructed. Finally, we integrate the gates and assemble the crucial ALU. Our strategy provides a facile strategy for assembling a large-scale complex DNA computer system, highlighting the great potential for programming the molecular behaviors of complicated biosystems.

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

“…Similar increases of speed are realized with polymerasemediated (rather than toehold-mediated) strand displacement on double 248 -or single-stranded 249 gates. The levels of gate integration are not dissimilar either.…”

Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

“…There are other polymerases with strand‐displacement activity that have been harnessed for constructing DNA circuits. For instance, Bst polymerase has been utilized to realize DNA arithmetic logic units with linear or branched structures; Bst 2.0 has been used to construct DNA logic circuits with single‐stranded gates . The primary difference between our work and these previous reports is that our work introduces a novel strand‐displacement mechanism to reduce strand complexity for situations where strands with similar function share a common domain, thereby extending the strand‐displacement design methodology, while these previous works mainly focus on the practical implementations of logic computation.…”

“…DNA polymerases are enzymes that synthesize DNA molecules from deoxyribonucleotides according to the templates, and widely used in DNA amplification . Besides, polymerases are also exploited in constructing DNA nanostructures for other applications including fluid transporting, logic computations, molecular clock, dynamic circuits, and biosensors . We notice that some polymerases have strand‐displacement activity, which provides the possibility for displacing the output strand from the O:S duplex without the branch‐migration process, and thereby polymerase‐triggered DNA strand displacement (PTSD) is introduced.…”

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

“…Similarly, to overcome the restrictions of poor integration efficiency, limited computing functions of DNA computing, Zhou's group constructed a DNA arithmetic logic unit (ALU) consisting of common DNA logic gates using the similar polymerase-induced strand displacement. [73] The use of enzymes brought highly efficient logic gates which are suitable for multiple cascades. Their work offers a facile method for assembling large-scale DNA computing system, enlightening the great potential for controlling the molecular behaviors of complicated biosystems.…”