A combined optical trapping and fluorescence experiment to unzip DNA. (a) A cartoon of the simplified experimental geometry (not to scale). A bead was tethered by a digoxygenin-based linkage (blue and yellow) to the coverglass surface through a DNA molecule, consisting of a long segment (black) joined to a shorter 15 base-pair strand that forms a duplex region (red). The bead (blue) was captured by the optical trap and force was applied to unzip the short duplex. Tetramethylrhodamine (TAMRA) dyes attached at the ends of the DNA strands provide a fluorescence signal (red dots). (b) Simultaneous records of force (red trace) and fluorescence, measured as the photon count rate (blue trace). Rupture occurred at t ≈ 2 sec at an unzipping force of 9 pN. The dye unquenched at the point of rupture, and later bleached at t ≈ 9 sec. See text for further details.