Innovative tool developed to observe interactions between DNA and enzymatic proteins

Scientists from the University of Washington cooperate with biotechnology company Illumina and have created a new tool - the single-molecule picometer-resolution nanopore tweezers, or SPRNT - to directly detect the single-molecule interactions between DNA and enzymatic proteins. This innovative tool provides a new platform to view and record these nanoscale interactions in real time. It provides fast and reliable characterization of the different mechanisms cellular proteins use to bind to DNA strands—information that could shed new light on the atomic-scale interactions within our cells and help design new drug therapies against pathogens by targeting enzymes that interact with DNA.
The new tool is reported on Sept. 28 in Nature Biotechnology. It is believed to be far more sensitive than other single-molecule tools in the market, for it can really pick up atomic-scale movements that a protein imparts onto DNA. The tool was developed when they were working on a related project.
The research team has been exploring nanopore technology to read DNA sequences quickly for a long time. They tried out a variety of molecular motors to move DNA through the pore when investigating nanopore sequencing. They discovered that their experimental setup was sensitive enough to observe motions much smaller than the distance between adjacent letters on the DNA. After research, they realized that they could detect minute differences in the position of the DNA in the pore and pick up differences in how the proteins were binding to DNA and moving it through the pore.
The SPRNT is sensitive enough to differentiate between the mechanisms that two cellular proteins use to pass DNA through the nanopore opening. One protein, which normally copies DNA, moves along the DNA one letter at a time as it guides DNA through the pore. The second protein, which normally unwinds DNA, instead takes two steps along each DNA letter, which they could pick up by tracking minute changes in the current, according to the report. The report also shows that these two steps involve sequential chemical processes that the protein uses to walk along DNA.
Through the tool you can see the underlying mechanisms and implications, which help you understand more about how life works and how better drugs can be developed.
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