Skip to main content
Dryad logo

Emergence of structures from parasitic species in a spatially distributed molecular system

Citation

Aubert-Kato, Nathanael; Gines, Guillaume; Rondelez, Yannick; Fujii, Teruo (2021), Emergence of structures from parasitic species in a spatially distributed molecular system, Dryad, Dataset, https://doi.org/10.5061/dryad.34tmpg4k7

Abstract

This dataset contains microscopy images from a microfluidic setup implementing a localized autocatalytic molecular system based on the PEN DNA toolbox. Due to the enzymatic nature of the catalytic process, a variety of parasitic species eventually emerge and compete with the legitimate molecular process for fuel. The behaviors observed range from the creation of large stable structures to that of small diffusing particles. Those results, along with the modularity of the molecular system, show that the proposed experimental setup can be used safely for further study of the evolution of parasitic behaviors at the molecular scale.

Methods

Reaction chambers were kept at 42C and monitored by an Olympus IX71 inverted microscope. 
We used two fluorescence sources: EvaGreen, a non-specific DNA-binding dye attaching to double-stranded species and Atto633 (red fluorophore, attached to minority beads).

We used an XY stage to take pictures of 30 regions of interest (10 per experimental settings) at 5-minute intervals. The regions of interest were manually selected by using the Atto633 fluorescence. We picked regions with at least one minority bead and 2 or more majority beads in close proximity to trigger a reasonably sized zone of enzymatic activity.

Usage Notes

It is recommended to use a software like Fiji to enhance the raw images.

Funding

Japan Society for the Promotion of Science, Award: JP17K00399

Japan Society for the Promotion of Science, Award: JP19KK0261