NanoDeep analysis method expands super-resolution microscopy applications

New analysis method from Karolinska Institutet increases the number of proteins that can be analyzed simultaneously

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NanoDeep analysis method expands super-resolution microscopy applications

SOLNA, Sweden—Researchers at the Karolinska Institutet have developed a new DNA-based analytical method that could contribute to the development of future drugs for cancers. A study, entitled “A DNA-nanoassembly-based approach to map membrane protein nanoenvironment,” has been published in Nature Nanotechnology.

While proteins on the surface of cells are the targets for most drugs, refined methods are needed to analyze the organization of these membrane proteins. The efficacy of most drugs in clinical use is attributable to their interaction with proteins on cell membranes; this makes understanding how these proteins operate essential, both in health and disease states.

Many of these cell membrane proteins are distributed into functional units, domains of nano-scale dimensions (i.e. 10-6 mm). Membrane proteins are analyzed using super-resolution microscopy, a technique which has been limited by the fact that only a small number of membrane proteins — usually three — could be analyzed simultaneously.

Researchers from the Karolinska Institutet have now developed a method that increases this number. This non-microscope-based method for analyzing entire populations of cells is called NanoDeep (nanoscale deciphering of membrane protein nanodomains).

“NanoDeep currently has a resolution in the 10 nanometer interval; that’s 10 billionths of a meter, which surpasses many other methods of super-resolution microscopy,” noted Ana Teixeira, a researcher in the Department of Medical Biochemistry and Biophysics at the Karolinska Institutet, and last author of the study. “NanoDeep has the potential to bring new insights into the regulation of membrane protein function.”

The NanoDeep method uses DNA analysis to translate information on membrane-protein organization, and there are no limits to the number of such proteins that NanoDeep can analyze simultaneously. This work has enabled the researchers to corroborate previous findings, and has also led to new discoveries.

The researchers were able to use the NanoDeep technology to describe protein environments surrounding the membrane receptor HER2 — a membrane protein that transmits information to proteins inside the cell. HER2 is over-represented in breast and other types of cancer, and a better understanding of HER2 will improve the chances of developing new drugs that can prevent most recurrences of such cancers.

“Our method makes the use of information on the spatial organizations of proteins at a nano-scale more accessible as a diagnostic tool in clinical tests. It can also be used as a tool for developing new kinds of drug designed to affect the function of membrane proteins,” added Elena Ambrosett, postdoctoral researcher and first author of the study.

This study was conducted with grants from the European Research Council, the Swedish Research Council, and the Knut and Alice Wallenberg Foundation.

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