Measuring DNA extension during unfolding in a centrifugal force microscope

Abstract

DNA in sperm cells can form compact toroids when bound with proteins from the protamine family. To study DNA folding and toroid formation, we have built a centrifugal force microscope (CFM) to unfold DNA and observe the intermediate folding states. In a CFM, micron-sized beads tethered to the sample by a DNA strand are placed into a microscope within a desktop centrifuge. The centrifuge applies a centrifugal force (a pseudoforce caused by inertia) to our sample, unfolding the DNA. Recording and analyzing the bead motion can yield information on the extension of the DNA over time and the intermediate stages of DNA condensation. Our CFM is operational at low centrifuge speeds, but we did not have a method for measuring the extension of the DNA. Here, we will discuss our progress in creating a program that gathers and analyzes video microscopy data from the CFM to measure extension in real time. This program will be useful in collecting data on the pathway of DNA condensation and for other force spectroscopy measurements with the CFM.