TABLE 1.

Quantitation of T-ag hexamer and double-hexamer formation on the set of oligonucleotides termed the asymmetric extensions of site II^a

Oligonucleotide and hexamer type H and DH	% Formation of hexamer and double hexamer in presence ofb:
	AMP-PNP	ADP	ATP	No nucleotide
64-bp core
DH	62.78	66.83	11.36	7.74
				2.39
				2.59
H	4.17	8.08	6.94	3.75
Total	66.95	74.91	18.30	16.46
48-bp site II + EP
DH	23.49	18.01	0.21	2.72
				0.50
				0.26
H	13.13	28.69	15.68	0.14
Total	36.62	46.70	15.90	3.62
47-bp site II + AT
DH	14.49	14.87	0.11	0.01
				2.57
H	19.58	40.32	13.77	2.89
Total	34.06	55.19	13.87	5.47
48-bp site II + EPm
DH	7.65	6.68		0.18
				0.25
				0.10
H	4.46	7.37	4.26	0.09
Total	12.11	14.05	4.26	0.61
47-bp site II + ATm
DH	3.85	2.30
				0.13
				0.07
H	2.78	4.89	2.61	0.34
Total	6.63	7.19	2.61	0.54
47-bp site IIm + AT
DH		0.49
H	6.20	5.85	0.99	0.27
Total	6.20	6.34	0.99	0.27
48-bp site IIm + EP
DH		0.19
H	3.52	3.01	1.52	0.04
Total	3.52	3.19	1.52	0.04
47-bp control
DH	0.14			0.05
H	0.75	2.17	0.49	0.38
Total	0.89	2.17	0.49	0.43

^aThe experiments in Fig. 9A (performed in the presence of AMP-PNP), Fig. 9B (performed in the presence of ATP), similar experiments conducted in the presence of ADP or in the absence of exogenous nucleotide (data not shown), and control experiments conducted with the 47-bp control oligonucleotide (Fig. 8, diagram 7, and data not shown) were quantitated with a Molecular Dynamics PhosphorImager. 

^bFor a given lane, the percentage of DNA in the hexamer (H) and double-hexamer (DH) species were determined. In those reactions conducted in the absence of nucleotide, intermediate species were detected running between the hexamer and double-hexamer bands. Numbers in italics indicate the percentage of DNA in these intermediate species.