TABLE II.

Mean structural parameters and 2DFS linewidths determined for the (Cy3)₂ dimer-labeled +15 “duplex” ss–dsDNA construct. The parameters determined from model analyses of linear absorbance and CD spectra are the mean resonant coupling $\overline{J}$, the mean twist angle ${\overline{\varphi }}_{AB}$, the mean tilt angle ${\overline{\theta }}_{AB}$, and the mean interchromophore separation ${\overline{R}}_{AB}$. The parameters determined from the 2DFS data are the inhomogeneous and homogeneous linewidths σ_I and Γ_H. Error bars were calculated based on a 1% deviation of the χ² function from its minimum (optimized) value.

Optimized parameters for (iCy3)2 dimer +15 “duplex” ss–dsDNA constructs
From absorbance and CD optimization					From 2DFS optimization
T (°C)	$\overline{J}$ (cm−1)	${\overline{\varphi }}_{AB}$ (deg)	${\overline{\theta }}_{AB}$ (deg)	${\overline{R}}_{AB}$ (Å)	σI (cm−1)	ΓH (cm−1)
1	493	78.3 + 0.3/−0.1	44.2 + 1.4/−0.4	3.49 + 0.9/−0.6	121.5 + 35.4/−32.4	105.1 + 22.2/−17.4
5	488	79.3 + 0.2/−0.1	39.3 + 0.7/−0.4	2.7 + 1.1/−0.4	212.7 + 36.8/−31.0	109.5 + 21.2/−17.9
15	532	80.7 + 0.2/−0.1	18.1 + 2.9/−2.1	3.7 ± 0.1	141.8 + 34.3/−33.4	149.4 + 19.7/−18.7
23	514	79.6 ± 0.2	10.2 + 6.4/−27	4.4 ± 0.1	136.7 + 45.8/−40.1	180.4 + 25.0/−20.3
35	496	76.0 ± 0.3	3.0 + 13/−19	5.5 ± 0.1	253.2 + 27.6/−25.3	91.8 + 14.0/−14.4
45	483	71.9 ± 0.4	7.7 + 8.5/−24	6.4 ± 0.1	268.4 + 31.8/−26.4	78.5 + 17.0/−12.0
55	467	70.4 ± 0.5	7.0 + 8.4/−22	6.8 ± 0.1	253.2 + 36.2/−33.9	60.8 + 18.7/−13.6
65	354	73.7 ± 0.6	5.4 + 11/−22	7.1 ± 0.1	217.8 + 31.4/−25.2	56.3 + 16.7/−14.1