DNA computing articles from across Nature Portfolio

Various methods, using DNA, have been reported for the recording of biomolecular interactions, but most are either destructive in nature or are limited to reporting pairwise interactions. Here the authors develop DNA-based motors, termed ‘crawlers’, that roam around and record their trajectories to allow the examination of molecular environments.

Examination of nucleation during self-assembly of multicomponent structures illustrates how ubiquitous molecular phenomena inherently classify high-dimensional patterns of concentrations in a manner similar to neural network computation.

Networks of interacting DNA oligomers have various applications in molecular biology, chemistry and materials science, however, kinetic dispersions during DNA hybridization can be problematic for some applications. Here, the authors reveal that limiting unnecessary duplexes using in-silico optimization can reduce in-vitro kinetic dispersions by as much as 96%.

Generic single-stranded oligonucleotides used as a uniform transmission signal can reliably integrate large-scale DNA integrated circuits with minimal leakage and high fidelity for general-purpose computing.

The heterogeneous and compartmentalized environments within living cells make it difficult to deploy theranostic agents with precise spatiotemporal accuracy. Zhao et al. demonstrate a DNA framework state machine that can switch among multiple structural states according to the temporal sequence of molecular cues, enabling temporally controlled CRISPR–Cas9 targeting in living mammalian cells.

The commercialization of DNA tagging is a growing trend that demonstrates the increasing practicality of this novel approach. This interdisciplinary technology is based on the distinctive characteristics of DNA as a molecule that can remain stable in varying environmental conditions and store data following appropriate preparation. Moreover, newly developed technologies could simplify DNA synthesis and the encoding of data within DNA. The implementation of DNA tagging presents distinctive benefits in comparison to conventional labelling techniques, including universal product code (UPC) barcoding, radio-frequency identification (RFID), quick response (QR) codes, and Bluetooth technologies, by surmounting the limitations encountered by these systems. The discourse pertains to extant DNA-tagging mechanisms along with prospective implementations in a wide range of domains, including but not limited to art, the metaverse, forensics, wildlife monitoring, and the military. The potential of DNA labelling in various contexts underscores the importance of continued research and development in this rapidly evolving field.

Molecular computing programmed with complementary nucleic acid strands allows the construction of sophisticated biomolecular circuits. Now, systems with partially complementary strands have been shown to enable more compact and faster molecular circuits, and may illuminate biological processes.

Neural networks can be implemented by using purified DNA molecules that interact in a test tube. Convolutional neural networks to classify high-dimensional data have now been realized in vitro, in one of the most complex demonstrations of molecular programming so far.

Fast and scalable molecular logic circuits have been constructed by spatially localizing DNA hairpins on DNA origami scaffolds.

Autocatalytic nanoparticles activated and deactivated by DNA 'programs' can trigger through-space molecular communication and give rise to collective particle behaviours.