A group of scientists in Japan have developed a computational DNA droplet that can recognise specific combinations of chemically synthesised microRNAs (miRNAs) which act as biomarkers of tumours.
Using these miRNAs as molecular input, the droplets can give a DNA logic computing output through physical DNA droplet phase separation.
The findings of Professor Masahiro Takinoue and his team at Tokyo University of Technology (Tokyo Tech) were published in Advanced Functional Materials.
He said: “If a DNA droplet can be developed which can integrate and process multiple inputs and outputs, we can use it in early disease detection as well as drug delivery systems.
“Our current study also acts as a steppingstone for research in developing intelligent artificial cells and molecular robots.”
Hot topic
Aqueous droplet formation by liquid-liquid phase separation (or coacervation) in macromolecules is a hot topic in life sciences research.
Of these various macromolecules that form droplets, DNA is interesting because it is predictable and programmable – qualities useful in nanotechnology.
In the recent study, the programmability of DNA was used to construct and regulate DNA droplets formed by coacervation of sequence designed DNAs.
Professor Takinoue, who is also the corresponding author, explained: “The applications of DNA droplets have been reported in cell-inspired microcompartments.
“Even though biological systems regulate their functions by combining biosensing with molecular logical computation, no literature is available on integration of DNA droplet with molecular computing.”
Experiments
Developing this DNA droplet required a series of experiments.
First, the team designed three types of Y-shaped DNA nanostructures called Y-motifs A, B, and C with 3 sticky ends to make A, B, and C DNA droplets.
Typically, similar droplets band together automatically while to join dissimilar droplets a special ‘linker’ molecule required.
So, they used linker molecules to join the A droplet with B and C droplet; these linker molecules were called AB and AC linkers, respectively.
In their first experiment they evaluated the ‘AND’ operation in the AB droplet mixture by introducing two input DNAs.
In this operation, the presence of input is recorded as one while its absence is recorded as zero.
The phase separation of AB droplet mixture occurred only at (1,1), meaning when both input DNAs are present, suggesting successful application of AND operation.
Breast cancer
Following this study, the scientists decided to introduce breast cancer tumour markers, miRNA-1 and miRNA-2, to AC droplet mixture as inputs for the AND operation.
The AND operation was successful implying that the computational DNA droplet identified the miRNAs.In subsequent experiments, the team demonstrated simultaneous AND as well as NOT operations in AB mixture with miRNA-3 and miRNA-4 breast cancer biomarkers.
Lastly, they created an ABC droplet mixture and introduced all the four breast cancer biomarkers to this solution.
The phase separation in ABC droplet depended on the linker cleavage resulting in a two-phase separation or a three-phase separation.
This property of ABC droplet enabled the researchers to demonstrate the ability to detect a set of known cancer biomarkers or detect markers of three diseases simultaneously.
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