Figure 3.

Analysis of Step Size and Stepping Kinetics

(A) DNA sequences are made of repeats of n AT base pairs followed by n GC base pairs where n=3, 4, or 5.

(B) A step-finding algorithm was used to measure FRET values and dwell times of the pauses for a single molecule. Three sequences with different GC content (from top to bottom: 48%, 50%, and 80%) were used for analysis. The step size was measured by counting the number of steps (n) until FRET reached a value of 0.3, and then dividing 10 by n.

(C) Histogram of the number of steps that occurred for each substrate.

(D) FRET histograms during unwinding; >50 molecules were used to build the histograms.

(E) FRET values obtained from 80 molecules from each substrate were combined to make the transition density plot (TDP).

(F) Gamma distribution fitting of the collected dwell times at each pause for >50 molecules.