Development of DNA-based fluorescent labeling for high-precision observation of protein movement: Tohoku University and Mie University aim to advance understanding of ALS and other diseases

A research team led by Associate Professor Shinsuke Niwa and Graduate Student Tomoki Kita of the Frontier Research Institute for Interdisciplinary Sciences at Tohoku University, in collaboration with Associate Professor Yuki Suzuki of the Graduate School of Engineering at Mie University, has developed a new fluorescent label for observing microscopic movements of proteins and other substances on a millimeter scale. Fluorescence-labeled tiny DNA origami blocks (FTOBs), a new type of fluorescent label made from DNA, are more resistant to photobleaching and blinking than conventional labels. They enable the observation of protein movements associated with neurological diseases, such as ALS (amyotrophic lateral sclerosis), with extremely high temporal resolution for a long period of time — in the order of milliseconds to several tens of minutes. FTOBs are designed for modular assembly, allowing them to be customized like building blocks. This versatility holds promise for a wide range of applications in research on various disease-related proteins. The study was published online in Cell Reports Physical Science.

Evidence indicates that impairment of kinesins is responsible in part for neurological diseases such as ALS. However, it remains unclear why these diseases occur, although half of the cells in patients with neurological disorders contain normal kinesins. To investigate the movements of kinesins and other proteins in detail, a technique that enables long-term observation of the protein movements with high temporal resolution in the order of milliseconds is required. Such a technique is an important tool for understanding the dynamic behavior of proteins and other molecules in research on neurological diseases and in other areas of life sciences. However, high-precision analysis using conventional fluorescent labels has been challenging due to issues such as photobleaching and blinking during observation.

DNA has a flexible structure, allowing for the free design and fabrication of extremely small structures using DNA origami. Structures constructed from DNA have very small sizes in the order of nanometers, which are suitable for research on proteins and other molecules.

The research group used this technique to develop the new fluorescent label FTOB, which is highly stable to light. FTOB achieved high photostability by integrating five fluorescent dyes at a distance of approximately 8.8 nanometers. By using this label, it is now possible to acquire high-precision videos at a millisecond scale, capturing more than 10 frames per second for over a minute without photobleaching or blinking. Furthermore, using FTOBs, the researchers created and observed a state in which disease-associated kinesins and normal kinesins were mixed, simulating the intracellular environment of a patient with a neurological disorder.

As a result, they discovered a new phenomenon in which kinesin alternately repeats deceleration and rapid acceleration. These findings provide important insights into understanding the mechanisms underlying the onset of neurological disorders. The DNA-based FTOB system has the feature of being freely modified in design, enabling detailed analysis of the interactions of various molecules including proteins. As a result, this system is expected to have broad applications in motion analysis, not only for kinesins but also for proteins associated with cancer and Alzheimer's disease as well as other diseases. Furthermore, high-time resolution observation using FTOBs may lead to the discovery of new biological phenomena that could not be captured with conventional observation methods.

Journal Information
Publication: Cell Reports Physical Science
Title: Modular photostable fluorescent DNA blocks dissect the effects of pathogenic mutant kinesin on collective transport
DOI: 10.1016/j.xcrp.2025.102440