DNA Computing Circuits Move Closer to Real-Time Function Inside Living Cells

A comprehensive review titled "From the Test Tube to the Cell: A Homecoming for DNA Computing Circuits?" published Mar. 4 in Intelligent Computing, a Science Partner Journal, highlights progress in operating DNA computing circuits for operation within living cells. According to the authors, dynamic nanodevices powered by DNA strand displacement reactions could soon enable real-time computing, sensing and actuation inside biological systems-and usher in a new era of "molecular robots" that interact with cellular environments.

DNA strand displacement circuits are a crucial aspect of dynamic DNA nanotechnology. They rely on DNA strand displacement reactions to perform logical and computational functions. DNA strand displacement circuits use toehold-mediated strand displacement, in which an invading DNA strand binds to a single-stranded toehold domain, initiating branch migration to displace an incumbent strand. Seminal DNA strand displacement systems, such as seesaw gates and hybridization chain reactions, facilitate complex logic operations and catalytic reactions, while cooperative gates require multiple inputs to trigger an output. These gates can be wired together to create circuits that mimic formal chemical reaction networks. Additionally, DNA strand displacement can also be linked to structural DNA nanodevices, such as DNA origami and DNA assemblies, enabling controlled structural changes and enhancing biological applications.

According to the authors, "DNA strand displacement reactions can be triggered by biological components such as nucleic acids, small molecules, proteins and ions." Nucleic acids, such as DNA and RNA, serve as direct inputs by leveraging complementary substrate designs, allowing applications in transcriptome analysis and live-cell monitoring. Input detection can be achieved through aptamers, which are single-stranded nucleic acid sequences that bind to targets or ligands with high affinity and specificity. To link aptamers to DNA strand displacement modules, various methods such as structure-switching aptamers, associative toeholds, hidden toeholds, remote toeholds, transient toeholds, chemical ligation, metallo-toeholds and DNAzymes have been developed to ensure precise signal transduction from biological targets to downstream circuits.

Currently, DNA strand displacement is primarily applied in vitro, and its application in vivo faces major challenges, including rapid degradation by DNA degrading enzymes. To enhance stability, researchers have explored structural modifications such as terminal protections like hairpins and protein binding sites, as well as chemical modifications like 2'-O-methylation. Since most cells naturally repel DNA, delivering these nanodevices into cells requires specialized techniques, such as transfection methods and transformation protocols. Once inside, cellular factors such as salt concentration, molecular crowding and heterogeneous environments influence strand displacement reactions. To overcome the limitations of direct delivery, researchers are also developing transcribable RNA nanodevices encoded into plasmids or chromosomes, allowing cells to express these circuits.

DNA strand displacement has been applied to the innovation of computational models. By integrating computational principles with DNA strand displacement, the structured algorithms of traditional computing can be combined with random biochemical processes and chemical reactions in biological systems, enabling biocompatible models of computation. In the future, DNA strand displacement may enable autonomously acting DNA nanomachines to precisely manipulate biological processes, leading to quantum leaps in healthcare and life science research.