Figure 1.

Round-trip time diffusivity analysis of DNA hairpin (color online). (A) A schematic of measurement shows that a single DNA hairpin is connected to double-stranded DNA handles that are attached to beads held by optical traps. The extension of the DNA construct is measured as the hairpin structure changes. (B) A representative section of an extension trajectory measured at constant force for hairpin 30R50/T4 is shown. The left inset shows the hairpin sequence, and the right inset shows the equilibrium probability density. Dashed lines indicate the locations of the unfolded (x_u) and folded (x_f) states. (C) The average round-trip times calculated from the extension trajectory with respect to reference points x_f (black) and x_u (red, inverted for ease of comparison) are qualitatively similar but do not agree quantitatively. (D) The diffusivity profile calculated from the round-trip time depends on the choice of reference point (black: reference point x_f, red: reference point x_u). Error bars represent SE. To see this figure in color, go online.