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Phage-bacteria interactions are typically studied in bulk culture, which obscures cell-cell differences. Here the authors study phage-bacteria interactions using single-cell transcriptomics, identifying cell subpopulations that resist infection through variable expression of multiple genes, without acquiring mutations.

The programmable and reliable hybridization of DNA strands has enabled the preparation of a wide variety of structures. This Review discusses how, in addition to these static assemblies, the process of displacing — and ultimately replacing — strands also makes possible the construction of dynamic systems such as logic gates or autonomous walkers.

Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, Cyriaque et al. use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level, providing insights into plasmid-bacteria dynamics.

A method called massively parallel PPI measurement by sequencing (MP3-seq) is developed for measuring protein–protein interactions at scale. MP3-seq uses DNA barcodes that are associated with specific protein pairs and provides a quantitative measure of interaction strength. Interactions between rationally designed heterodimers and elements conferring interaction specificity were investigated using MP3-seq.

Toe-hold-mediated strand displacement (DSD) is a widely used molecular tool in applications such as DNA computing and nucleic acid diagnostics. Here the authors characterize dozens of orthogonal barcode sequences that can be used for monitoring the output kinetics of multiplexed DSD reactions in real-time using a commercially-available portable nanopore array device.

mRNA therapeutics are revolutionizing the pharmaceutical industry. In this study, the authors characterize 5’UTR-regulated translation in cell types relevant for mRNA therapies and with fully random 5’UTRs, and show that 5’UTRs optimized via deep learning support high performance on mRNA-encoded gene editors.

Storage technology based on DNA is emerging as an information dense and durable medium. Here the authors use machine learning-based encoding and hybridization probes to execute similarity searches in a DNA database.

Here the authors characterize the sequence-specific effect of an anticancer compound on mRNA cleavage, providing insights into the mechanism of mRNA 3′ processing.

DNA is an attractive digital data storing medium due to high information density and longevity. Here the authors use millions of sequences to investigate inherent biases in DNA synthesis and PCR amplification.

Ribosome loading is predictably controlled through design of 5′ UTR sequences.

By adapting DNA strand displacement and exchange reactions to mammalian cells, DNA circuitry is developed that can directly interact with a native mRNA.

Gene expression profiling remains cost-prohibitive and challenging to implement in a clinical setting. Now, a molecular computation strategy for classifying complex gene expression signatures has been developed. Classification occurs through a series of molecular interactions between RNA inputs and engineered DNA probes designed to implement a relevant linear classification model.

SPLiT-seq single-nucleus RNA sequencing of the developing human cerebellum reveals cell-type complexities and prolonged maturation compared to mouse with important disease implications.

Neural networks have become a useful approach for predicting biological function from large-scale DNA and protein sequence data; however, researchers are often unable to understand which features in an input sequence are important for a given model, making it difficult to explain predictions in terms of known biology. The authors introduce scrambler networks, a feature attribution method tailor-made for discrete sequence inputs.

A major bottleneck in using DNA as a data storage medium is the slowness of sequencing. Here the authors decode 1.67 megabytes of information using a portable nanopore platform with an assembly strategy for increased throughput.

Microcompartments with a temperature-responsive membrane are used to stably localize DNA-encoded files, which enables parallel, repeated polymerase-chain-reaction-based random access and DNA file sorting using fluorescent barcodes.

200 MB of digital data is stored in DNA, randomly accessed and recovered using an error-free approach.

Fast and scalable molecular logic circuits can be created through the spatial organization of DNA hairpins on DNA origami scaffolds.

Chemical controllers made from DNA can be programmed to implement any dynamic behaviour compatible with chemical kinetics.

A molecular probe has been designed that distinguishes double-stranded DNA with single base-pair specificity. In this approach, two destabilizing bubbles, in which the base pairs are mismatched, are generated for each point mutation in the target DNA.

A DNA nanodevice performs pathfinding search and computes the solution of two-dimensional DNA origami puzzles.

Using a combination of behavioral and physiological approaches, the authors show that ON and OFF motion detection pathways in Drosophila exhibit distinct temporal tuning properties. Computational modeling suggests that these asymmetric tuning properties improve the fly's ability to reliably estimate velocity in natural environments.

Single-cell transcriptomics of bacteria is challenging. microSPLiT is a high-throughput method for single-cell RNA sequencing of both Gram-positive and Gram-negative bacteria using combinatorial barcoding without the need for specialized equipment.

This article reviews recent progress in the development of cellular DNA nanotechnology, highlighting key potential applications such as DNA-based imaging probes, smart therapeutics, and drug delivery systems.