Abstract
We have developed a novel method to follow the dynamics of DNA interacting with the cellular environment in vivo using two-color correlation microscopy. A DNA probe is end-labeled with two quantum dots and transfected into an axenic strain of Dictyostelium discoideum. The motion of the quantum dots is observed with two-color fluorescence video microscopy. The computed time correlation functions of this two-particle motion reflect the fluctuations of the DNA probe as a result of its interactions with the cellular environment. Substantial differences between live cells and dead yet structurally intact cells point to a strong coupling of active, motor-driven fluctuations in the cell to the DNA probe. This suggests that the motion of native cellular DNA may similarly be driven by active processes instead of relying on purely thermal passive fluctuations. We also note that the difference between the autocorrelations of the center of mass motion and the relative motion of the two quantum dots is a sensitive measure for the effective length of the DNA probe on a length scale around one persistence length (∼ 50 nm). This paves the way for experiments with more complex DNA probes that can bind to intracellular proteins, and report single-molecule binding events through apparent length changes and consequently changes in this correlation measure.
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