A Korean research team has become the first to reveal that fluorescent "tags," widely used to observe minute movements at the nanometer (nm, one-billionth of a meter) scale inside living organisms, can actually damage the binding between biomolecules. The team is credited with elevating the reliability of ultra-precise life science research by identifying the cause of this side effect and even proposing new nanomaterial design standards to block the interference.
The Ulsan National Institute of Science and Technology (UNIST) announced on the 9th that a joint research team led by Professor Lee Ja-il of the Department of Biological Sciences and Professor Park Jong-nam of the Department of Energy and Chemical Engineering had identified that a polymer material on the surface of commercial "Quantum Dots" disrupts the binding of proteins and DNA, and developed a surface design technology to prevent this.
Quantum dots are brighter and longer-lasting than ordinary fluorescent dyes, and have drawn attention in bio-medical research as fluorescent markers attached to specific proteins to track their movements. Typically, the surface of commercial quantum dots is coated with a polymer material called "polyethylene glycol (PEG)" to improve dispersibility in aqueous solutions and to bind well with target proteins (antibodies).
However, when the team observed the interaction between "XPA," a DNA damage repair protein, and DNA, they found that the two materials separated from each other as the concentration of quantum dots increased. The main culprit behind the dissociation of the binding was none other than PEG, the surface coating material. When the proportion of PEG on the quantum dot surface was excessively high, the observation tool itself caused "hidden interference" that actually pulled apart the binding of the observation target. The same phenomenon was also confirmed in another repair protein, "UV-DDB."
In response, the team completely redesigned the polymer on the quantum dot surface. Tracking the "golden cross" that could block protein-DNA binding interference while maintaining the quantum dot's inherent dispersion stability and fluorescent characteristics, they found the optimal standard: lowering the proportion of PEG-based components to below 7%.
Using quantum dots with a reduced PEG ratio, the team also overcame the limitations of existing observation methods. They newly demonstrated that when the XPA protein searches for DNA damage sites, it mainly uses a "three-dimensional collision" method, in which it wanders through the solution and directly collides with and binds to defect structures, rather than a "one-dimensional diffusion" method, in which it slides along the strand.
"By precisely controlling the type and ratio of quantum dot surface materials, we preserved brightness and colloidal stability while dramatically reducing biological interference," Professor Park Jong-nam explained. "This surface design strategy can be applied broadly to the development of various nanoparticle-based bio-research tools, not just quantum dots."
"We have systematically confirmed for the first time that commercial quantum dots are not merely observation tools but can shake the very binding of proteins and DNA," Professor Lee Ja-il stressed. "The quantum dots developed this time can be used to observe the movement of single molecules more accurately while maintaining the original interactions of biomolecules."
Meanwhile, the study, in which researchers Kim Young-seo (Department of Biological Sciences) and Kim Hye-rim (Department of Energy and Chemical Engineering) participated as co-first authors, was conducted with support from the National Research Foundation of Korea (NRF), the Institute for Basic Science (IBS), and the Ministry of Trade, Industry and Energy (MOTIE). The results were published online on the 3rd of last month in "Nano Convergence," an international academic journal in the nanotechnology field.
