Stretched, Oriented DNA Arrays (SODA) for Fluorescence Based Single-Molecule Experiments in Complex Environment

All biochemical and biophysical processes that support cellular activity take place in complex, crowded environments. Up to 30% of the weight of a cell consists of proteins, DNA and other large biological macromolecules. Consequently, 1-dimensional protein motions along DNA while replication or transcription have to be studied and understood in the context of a DNA molecule that is not naked, but instead bound by a wide variety of obstacles - roadblocks. Inspired by previous, pioneering work on DNA curtains, we used the intrinsic propriety of some macromolecules and polymers to create self-assembled, organized structures, adapted for visualization using TIRF microscopy of interactions between genome processing enzymes and roadblocks in crowded environment.