Table 1.

Effectiveness of specific compounds is environment sensitive and can be used in combination to minimize photophysical processes in the DNA system

	DNA system
	Cy dyes				Alexa dyes
	Total ton (s)	Total toff (s)	% Total ton (%)	ntransitions (s−1)	Total ton (s)	Total toff (s)	% Total ton (%)	ntransitions (s−1)
No compounds	6.5	4.0	62.9	0.3	5.5	19.1	29.8	0.4
2 mM COT	10.2	6.1	63.1	0.2	9.2	13.3	46.9	0.2
2 mM NBA	4.9	0.3	96.6	0.2	5.9	0.2	94.6	0.2
2 mM Trolox	25.8	2.9	85.3	0.1	24.6	4.4	80.9	0.1
All compounds	16.6	1.0	93.6	0.1	24.1	1.7	91.0	0.1

Values of Total t_on, Total t_off, the percent time each of the systems investigated is in the nonzero FRET state before photobleaching, % Total t_on (Total t_on/Total t_on + Total t_off), and the number of transitions per second, n_transitions, are shown in absence and presence of 2 mM COT, 2 mM NBA, or 2 mM Trolox separately and in combination (illumination intensity = 0.65 kW/cm²). As described in the Materials and Methods, the reported values of Total t_on and Total t_off were calculated by fitting and the percent time in nonzero FRET states, % Total t_on, was calculated by dividing the total dwells in the zero FRET state by the total length of the smFRET time trace before photobleaching. In each case a minimum of 1650 number of transitions were observed and fitting resulted in R² values > 0.995.