Empirical design parameters determine in-cell performance
It could lead to an artificial sensing system that could control a cell’s behavior in response to such stimuli as the presence of toxins or the development of cancer. The research uses DNA strand displacement, a technology that has been widely used outside of cells for the design of molecular circuits, motors and sensors. Researchers modified the process to provide both “AND” and “OR” logic gates able to operate inside the living cells and interact with native messenger RNA (mRNA).
The tools they developed could provide a foundation for bio-computers able to sense, analyze and modulate molecular information at the cellular level. “The whole idea is to be able to take the logic that is used in computers and port that logic into cells themselves,” said Philip Santangelo. “These devices could sense an aberrant RNA, for instance, and then shut down cellular translation or induce cell death.”
Strand exchange-based OR and AND logic gates work in mammalian cells.
Strand displacement reactions are the biological equivalent of the switches or gates that form the foundation for silicon-based computing. They can be programmed to turn on or off in response to an external stimuli such as a molecule. An “AND” gate, for example, would switch when both conditions were met, while an “OR” gate would switch when either condition was met. In the switches, a fluorophore reporter molecule and its complementary quenching molecule were placed side-by-side to create an “off” mode. Binding of RNA in one of the strands then displaced a portion of nucleic acid, separating the molecules and allowing generation of a signal that created an “on” mode. 2 “on” modes on adjacent nucleic acid strands created an “AND” gate.
“Demonstrating individual logic gates is only a first step,” said A/Prof Georg Seelig. “In the longer term, we want to expand this technology to create circuits with many inputs, such as those we have constructed in cell-free settings.” They used ligands designed to bind to specific portions of the nucleic acid strands. “We had to chemically change the probes to get them to work inside the cell and to make them stable enough inside the cells,” said Santangelo. “We found that these strand displacement reactions can be slow within the cytosol, so to get them to work faster, we built scaffolding onto the mRNA that allowed us to amplify the effects.”
Endogenous mRNA and mMTRIPS can serve as scaffolds for strand exchange reactions
Using strands of nucleic acid, scientists have demonstrated basic computing operations inside a living mammalian cell. Shown examining a cellular “AND” gate are associate professor Philip Santangelo and research scientist Chiara Zurla. Credit: Rob Felt, Georgia Tech
The nucleic acid computers ultimately operated as desired, and the next step is to use their switching to trigger the production of signaling chemicals that would prompt the desired reaction. Cellular activity is normally controlled by the production of proteins, so the nucleic acid switches will have to be given the ability to produce enough signaling molecules to induce a change. “We know the concentrations of chemicals and the design requirements for individual components, so we can now start putting together a more complicated set of circuits and components.”
Cells know how to sense toxic molecules and the development malignant tendencies, and to then take action. But those safeguards can be turned off by viruses or cancer cells that know how to circumvent natural cellular processes. “Our mechanism would just give cells a hand at doing this,” Santangelo said. “The idea is to add to the existing machinery to give the cells enhanced capabilities.” http://www.newswise.com/articles/scientists-demonstrate-basics-of-nucleic-acid-computing-inside-cells
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