A nanofluidic toolbox to study DNA-Protein interactions in DNA repair and genome organization

Research Project, 2026 – 2030

DNA contains all information needed to create life as we know it. To utilize this information, proteins interact with DNA in many ways, including replication and transcription. DNA-protein interactions are also crucial for packaging and repairing DNA. Single molecule techniques have revolutionized the understanding of DNA-protein interactions.Here we develop a state-of-the-art nanofluidic toolbox to analyze single DNA-protein complexes. Nanochannels have the unique advantage that both ends of long DNA are free and interactions involving more than one long DNA molecule can be studied. It is also a high throughput method where thousands of molecules can be analyzed per hour. Two technical developments will be implemented. 1) The use of Nanofluidic Scattering Microscopy to study DNA-protein complexes, label-free, in nanochannels. 2) A toolbox to create a library of long DNA with tailored sequence and end-structures.We will explore two important biological problems. First, how broken DNA is repaired. This is a delicate process since any mistake can lead to cell-death or disease-causing genetic rearrangements. We will study the first steps of repair and pinpoint how the preferred repair pathway is selected. Second, how bacteria package their genomes. Since bacteria are diverse, many different proteins are involved that have different function and regulation. We will select strategic examples from different organisms and reveal molecular details of the processes.