Researchers at the Indian Institute of Science (IISc) have implemented an advanced microscopy technique to visualise multiple biomolecules inside the nucleus of a cancer cell simultaneously at incredibly high resolution. The biomolecules they visualised include critical components of the cell’s transcription machinery and proteins that provide structural support to the nucleus – providing one of the first detailed maps of nuclear organisation.
The human body is composed of trillions of cells. Each cell is an intricately organised meshwork of millions of proteins, nucleic acids, and many other molecules vital for the cell’s health. “Building novel technologies to visualise many biomolecules in individual cells is crucial to push the boundaries of biological research,” says Mahipal Ganji, Assistant Professor at the Department of Biochemistry (BC) and corresponding author of the study published in Nature Communications. Conventional imaging techniques, however, allow scientists to visualise only two or three biomolecules in each cell at a time.
In the study, the researchers turned to a microscopy technique called DNA-Points Accumulation for Imaging in Nanoscale Topography (DNA-PAINT), which allows for the visualisation of biomolecules inside cells at incredible detail – far beyond the limits of conventional microscopes. It uses small fluorescent DNA fragments or tags that briefly attach to specific targets inside the cell and light up like tiny, blinking signals when a laser beam is shined on them.
Different cellular components can be labelled with unique DNA tags, which can be tracked to build very sharp images of tiny targets. So far, however, researchers have only been able to tag and observe 2-3 molecules at a time. “Conventional techniques are limited to only seeing three molecular species. Seeing many more would pave the way for detailed biological insights into cellular organisation,” says Micky Anand, PhD student at BC and co-first author.
In the current study, the IISc team made several significant improvements to DNA-PAINT. They were able to create tags that could bind to 12 different targets simultaneously – five of these were able to stick to the target molecules faster and for much longer, allowing sharper and clearer images showing details as tiny as 3-5 nanometers in size. Using strongly binding tags reduces the energy of the laser beam required to visualise the biomolecules, leading to reduced damage to the DNA tags as well as cells.
The team was also able to significantly speed up the imaging process. Visualising even one biomolecule would take hours in the initial days of DNA-PAINT; using their modified technique, the team was able to visualise nine different targets in less than four hours.
The new technique also allowed the researchers to observe how the cells re-organise proteins and biomolecules when an important cellular process like transcription is blocked.
“Understanding how protein distributions change in diseased cells could open up new ways to detect illness before symptoms appear,” says Abhinav Banerjee, a BC PhD alumnus, now a postdoctoral researcher at the Janelia Research Campus (HHMI) and co-first author of the study. “By mapping the precise locations of diverse biomolecules at the nanometer scale, we can begin to uncover how they interact with one another and how these relationships are altered in disease.”
Nature Communications
High-speed multiplexed DNA-PAINT imaging of nuclear organization using an expanded sequence repertoire
22-Apr-2026