Abstract
We constructed a microscope-based instrument capable of simultaneous, spatially coincident optical trapping and single-molecule fluorescence. The capabilities of this apparatus were demonstrated by studying the force-induced strand separation of a dye-labeled, 15-base-pair region of double-stranded DNA (dsDNA), with force applied either parallel ('unzipping' mode) or perpendicular ('shearing' mode) to the long axis of the region. Mechanical transitions corresponding to DNA hybrid rupture occurred simultaneously with discontinuous changes in the fluorescence emission. The rupture force was strongly dependent on the direction of applied force, indicating the existence of distinct unbinding pathways for the two force-loading modes. From the rupture force histograms, we determined the distance to the thermodynamic transition state and the thermal off rates in the absence of load for both processes.
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Acknowledgements
We thank the entire Block lab for helpful discussions and J. Shaevitz for assistance with energy landscape calculations. This work was supported by grants to S.M.B. from the National Institutes of Health. P.M.F. acknowledges support from a National Science Foundation predoctoral fellowship and a Lieberman Award Fellowship; A.M.E. was supported by the Stanford Biophysics Training Grant from the National Institutes of Health; and M.J.L. was supported by a postdoctoral fellowship from the Jane Coffin Childs Foundation.
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Lang, M., Fordyce, P., Engh, A. et al. Simultaneous, coincident optical trapping and single-molecule fluorescence. Nat Methods 1, 133–139 (2004). https://doi.org/10.1038/nmeth714
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DOI: https://doi.org/10.1038/nmeth714
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