Figure 1.

The average time for the TF to reach the target site (measured in seconds) as a function of DNA crowding in the case of mobile obstacles. Note the differences between scales of the y-axis, e.g. for 1 lacI molecule it takes in the range of tens of minutes to locate the target site, while for 100 copies the search time is in the range of seconds. The number in the inset represents the Pearson coefficient of correlation between crowding and the mean of the search time. The values indicate the crowding is highly correlated with the search time, in the sense that higher crowding on the DNA leads to higher search times. We used notched boxplots to represent the data, where: (1) the line in the box represents the median, (2) 50% of the data (the interquartile range IQR) occurs between the lower edge of the box (first quartile Q1) and upper edge of the box (third quartile Q3), (3) the lower whisker marks the maximum between (Q1 − 1.5 × IQR) and the lowest point in the data set, (4) the upper whisker marks the minimum between (Q3 + 1.5 × IQR) and the highest point in the data set, (5) the crosses represent the outliers and (6) the notches indicate the confidence intervals for the medians (if the notches of two medians do not overlap, the medians are significantly different at a 95% confidence level). Note that to enhance the visibility, the boxplots are positioned equidistant although the crowding levels are not. We considered four cases with respect to the number of lacI molecules, namely: (A) 1 molecule, (B) 10 molecules, (C) 100 molecules and (D) 1000 molecules.