Researchers Develop ‘NanoporeTERs’ That Could Potentially Allow Computers to Directly Read Cells

Researchers have created new and more efficient genetic reporter proteins to detect specific proteins in cells, a step which is believed to help in the study of genetic material and intracellular processes, engineered or otherwise. Genetically encoded reporter proteins are of much use in the fields of biotechnology. These reporter proteins help detect certain proteins and decode engineered genetic circuits. However, conventional reporter proteins rely on the fluorescence of protein molecules, which makes it difficult to detect some strains. However, researchers at the University of Washington and Microsoft have developed reporter proteins that can be read by a ‘nanopore sensing device’.

Researchers call this new reporter protein ‘nanopore-addressable protein tags engineered as reporters’ (NanoporeTERs, or NTERs). The team has developed 20 such NTER tags and stored them in a library.

The research report was published in Nature Biotechnology. Reporter proteins can help researchers gather data about cell processes and anomalies. Conventionally, only optical proteins that showed fluorescent effects could be detected through the trial-and-error method. The maximum number of protein strands that could be simultaneously studied were also limited. This largely limited cellular-level research.

However, the new synthetic proteins are secreted outside a cell to gather information about the cellular environment. They carry distinct amino acid “barcodes” that respond to a nanopore detector. For the study, researchers used the Oxford Nanopore Technologies MinION device. With these reporter proteins, it is also possible to simultaneously read more protein strands, which give at least 10 times more multiplexing opportunities.

NTERs are proteins with charged “tails” that attract them to the sensors of a nanopore through an electric field. Researchers, then, use machine learning to decode these electrical signals and classify them into NTER barcodes.

“This is a fundamentally new interface between cells and computers,” a report by EurekAlert quoted Jeff Nivala, one of the nine authors and a University of Washington Research Assistant Professor, as saying.

Lead Co-author Karen Zhang saw a potential to expand these NTERs beyond 20 tags. “We are currently working to scale up the number of NanoporeTERs to hundreds, thousands, maybe even millions more,” he said in the same report.

NTERs can change the way we detect diseases or target therapeutics to specific areas in the body. And “debugging complicated genetic circuit designs” is another field that will benefit from this research.