Scientists have made a giant leap towards creating a new method of gene sequencing a DNA strand's base using a nanoscopic hole, and they have shown this technique could also be used to study the structure of proteins and provide insight into disease.
Current methods that allow scientists to look at proteins in this way are extremely tedious and labor-intensive, the University of Pennsylvania reported. These methods also require the protein to be modified, which could skew the results and prevent the proteins from being observed in their natural state. This new method provides a simpler way to look at protein structure without having to alter the protein itself, opening up the door for groundbreaking insights into disease.
The technique is based on one used to distinguish the bases in a strand of DNA by the different percent of the aperture they block as they move through a nanoscopic pore. Electrons surrounding the pore measure changes in ion flow caused by varied silhouettes designed for ionic liquid to pass through, allowing scientists to correlate these readings to each base. Researchers are now looking at ways to use this technique for other applications, such as studying protein structures.
"There are many proteins that are much smaller and harder to manipulate than a strand of DNA that we'd like to study," said Jeffrey Saven, a professor in Penn Arts & Sciences' Department of Chemistry. "We're interested in learning about the structure of a given protein, such as whether it exists as a monomer, or combined with another copy into a dimer, or an aggregate of multiple copies known as an oligomer."
A team of researchers used silicon nitride nanopores to look at the protein GCN4-p1. The dimer version of the protein was "zipped" together into a cylindrical form, while the monomer version was unzipped to be more string-like. The researchers placed both the zipped and unzipped forms of the protein into an ionic fluid, and passed them through the pores.
"The dimer and monomer form of the protein block a different number of ions, so we see a different drop in current when they go through the pore," said postdoctoral researcher David Niedzwiecki. "But we get a range of values for both, as not every molecular translocation event is the same."
The ability to determine whether or not samples of these proteins are aggregated could allow scientists to gain insight into the progression of certain diseases.
"Many researchers have observed these long tangles of aggregated peptides and proteins in diseases like Alzheimer's and Parkinson's, but there is an increasing body of evidence that is suggesting these tangles are occurring after the fact, that what are really causing the problem are smaller protein assemblies. Figuring out what those assemblies are and how large they are is currently really hard to do, so this may be a way of solving that problem," Saven concluded.
The findings were published in a recent edition of the journal ACS Nano.
