Optical Nanoscopy Images DNA Naturally Fluorescing

A novel imaging tool that is able to capture images of DNA naturally fluorescing could advance the study of individual biomolecules and help uncover global patterns of gene expression.

Existing methods for imaging DNA and other genetic material rely on fluorescent labeling of biomolecules. Because it is virtually impossible to label every nucleotide, the resolution of the most widely used nanoscopy technologies is limited to a few tens of nm, which may contain tens of thousands of base pairs.

A powerful Northwestern University imaging tool measures the structure of isolated chromosomes without the use of fluorescent labels. Courtesy of Northwestern University.

A novel label-free optical nanoscopy capable of molecular imaging with 6-nm resolution, developed by a research team at Northwestern University, will enable scientists to study DNA, chromatin and proteins in cells in their natural environment, without the need for fluorescent labels.

The team discovered that most biopolymers such as DNA and proteins, which until recently had been considered “dark” in the visible regime, exhibited stochastic photoswitchable autofluorescence when illuminated by visible light due to the ground-state depletion (GSD) recovery phenomenon.

The team developed a technique, called Spectroscopic Intrinsic-Contrast Photon-Localization Optical Nanoscopy (SICLON), based on this newly discovered physical effect. SICLON is able to image DNA, chromatin, and proteins without labeling. The technology combines time-resolved stochastic photon localization with simultaneous spectroscopic molecular-signature-carrying intrinsic fluorescence detection.

“Our technology will allow us and the broader research community to push the boundaries of nanoscopic imaging and molecular biology even further,” professor Vadim Backman said.

For decades, textbooks have stated that macromolecules within living cells, such as DNA, RNA and proteins, do not have visible fluorescence on their own.

“People have overlooked this natural effect because they didn’t question conventional wisdom,” said Backman. “With our superresolution imaging, we found that DNA and other biomolecules do fluoresce, but only for a very short time. Then they rest for a very long time, in a ‘dark’ state. The natural fluorescence was beautiful to see.”

The researchers now are using the label-free technique to study chromatin, the bundle of genetic material in the cell nucleus, to see how it is organized.

“Insights into the workings of the chromatin folding code, which regulates patterns of gene expression, will help us better understand cancer and its ability to adapt to changing environments,” Backman said. “Cancer is not a single-gene disease.”

The talk Label-Free Super-Resolution Imaging of Chromatin Structure and Dynamics was part of the symposium Optical Nanoscale Imaging: Unraveling the Chromatin Structure-Function Relationship which was held on February 17, 2017 at the AAAS 2017 Annual Meeting.