Intramolecular dynamics of linear macromolecules by fluorescence correlation spectroscopy

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Abstract
A theoretical description of the dynamics of DNA molecules and actin filaments in solution as measured experimentally by fluorescence correlation spectroscopy is provided and compared to recent experimental results. Particular attention is paid to the contribution of the intramolecular dynamics to the fluorescence correlation function. Using a semiflexible chain model, a theoretical expression is presented for the fluorescence correlation spectroscopy correlation function. The dependence of this function on various model parameters, such as chain length, persistence length, and fluorescence label density, is discussed. Our investigations show that the intramolecular dynamics provides a significant contribution or even dominates the correlation function as soon as the longest intramolecular relaxation time significantly exceeds the shortest experimentally accessible time. Correspondingly, the shape of the correlation function changes considerably. Approximate analytical expressions are provided, which are in qualitative agreement with the exact theoretical solutions as well as experimental results, for both DNA and actin filaments. Our approach is in agreement with the predictions of the Zimm model, in the limit of very flexible polymers, as well as the predictions of semiflexible polymer models with respect to the intramolecular dynamics in solution.