Fig. 5: E. coli can be trapped by DNA networks formed by unprotected particles.

a Schematic representation of trigger-induced E. coli entrapment. Once activated by the addition of the trigger strand, particles assemble into a sticky DNA network. Swimming E. coli stick to, or become embedded in the aggregates, which renders them immobile. b Confocal micrographs demonstrating E. coli entrapment. Core C-stars (fluorescein) are shown in cyan, E. coli (mKate2) in red. Scale bar 10 μm. c Top: trigger-induced E. coli entrapment as quantified through a motility parameter σ (extracted from microscopy videos, see Methods and main text for definition) for samples with and without the addition of trigger. The smaller and non-uniform σ-values detected in the presence of the trigger confirm the ability of the DNA aggregates to hinder E. coli motion. See Supplementary Fig. 16 for the σ-maps extracted at different incubation stages, where the absence of significant signal from the early-time maps confirms that Brownian motion from the particles has a comparatively negligible effect on σ. Bottom: epifluorescence micrographs in the DNA (cyan) and E. coli (red) channels collected in the corresponding fields of view. Scale bar 20 μm. d Time-trace of the frame averaged motility parameter \(\bar{\sigma }\) for samples of E. coli and DNA particles (with and without trigger) and a control sample in which no DNA particles were present. The increase in \(\bar{\sigma }\) observed in the presence of particles can be ascribed to bacterial growth, as confirmed in panel e and Supplementary Fig. 17. While \(\bar{\sigma }\) continues to grow steadily in the sample with non-triggered particles, as more moving bacteria are generated, DNA-aggregation and E. coli entrapment cause the curve to plateau. e Normalized fluorescence intensity of E. coli-expressed mKate2 protein as extracted from epifluorescence images for the samples in panel (d). An increasing signal indicates bacterial growth, which occurs in the presence of DNA particles but is absent for the control DNA-only sample, suggesting that E. coli can use the DNA particles as a food source (see also Supplementary Fig. 17). Data shown in panels (b–e) was acquired in two independent experiments.