TABLE 3.

Interaction of RNAP holoenzyme with fork junction probes

Free energy of RNAP binding to the −12/−7, −12/−3, and −2+/2 single-stranded segments calculated using equation ΔG = −RT ln(K_d(1)/_d(2)).

Assayed segment	Probe	Kd	Kd (1)/Kd (2)	−ΔG	−ΔG/base
		nm		kcal/mol	kcal/mol
−12/−7	1, [−38/−13]	170	28,000	6.1	1.02
	2, [38/−7][−38/−13]	0.0061
−6/−3	1, [−38/−7][−38/−12]−35mut	2.1
	2, [−38/−3][−38/−12]−35mut	0.01	210	3.2	0.80
−2/+2	1, [−26/−3][−26/−12]	0.46
	2, [−26/+2][−26/−12]	0.05	9.2	1.3	0.33
	1, lacUV5[−26/−3][−26/−12]	5.3	13	1.5	0.38
	2, lacUV5[−26/+2][−26/−12]	0.39