Karymov et al. 10.1073/pnas.0407210102.

Supporting Information

Files in this Data Supplement:

Supporting Figure 5
Supporting Text
Supporting Figure 6
Supporting Table 1
Supporting Figure 7




Fig. 5. The alternate labeling design for enhanced sensitivity to folding (at the expense of sensitivity to migration) (a) and the time trajectories (b and c) for the FRET efficiency. The labeling scheme is shown in a. Homologous regions capable of branch migration are indicated by thick red lines. Cy3 and Cy5 dyes are indicated by green and red circles, respectively. Experimental data for FRET efficiencies at 10 mM (b) and 0.3 mM Mg2+ (c) are shown.




Supporting Figure 6

Fig. 6. Cumulative FRET trajectory data obtained at different concentrations of Mg2+ cations. (a) Series of averaged time-dependent trajectories shown for the same time interval (1.5 s.). Color dotted and dashed horizontal lines correspond to expected FRET values (see Fig. 1c). (b) The histogram shows FRET plateau values collected from a series of independent experiments performed at 10 mM Mg2+. Red curves show the resolved peaks. Arrows point to the positions of peaks of these distributions. The green bell-shaped curve is a Gaussian approximation of the overall histogram. (c) The histogram shows FRET steps values collected from a series of independent experiments performed at 0.3 mM Mg2+.





Fig. 7.

 The Monte Carlo computed square of the time average width of the fluctuation of the efficiency (dE2 = <E2>t – <E>t2) as a function of Nhops(= tbin/tR), where tR is the residence time. (Insets) Typical Monte Carlo single-molecule efficiency-time behavior at Nhops = 0.1 (large dE2) and Nhops = 10.0 (small dE2). For comparison, the dotted line is the constant DE2, which is the square deviation of the different efficiencies Ei at the six sites and the dashed line is DE2/Nhops.




Table 1. The dependence of the average time length of plateaus on the concentration of Mg2+

Concentration of Mg2+, mM

Average time length of plateau (ms) ± SEM (ms)

SD, ms

0.3

19 ± 0.6

22

1

22 ± 1.0

30

2

28 ± 1.2

35

5

38 ± 2.7

54

10

71 ± 5.4

80