Table 2.

Comparison of Structural Features of 4-OHEN-C, A^a and G Adducts with the Unmodified Duplex

	Adjacent Base Pairb	Number of Adduct Hydrogen Bondsc	Stacking Energy Differenced(kcal/mol)	Bend Angle Differencee (degrees)	Major Groove Distortionf (Å)	Minor Groove Distortionf (Å)
Color code: most distorted, red; somewhat distorted, orange; least distorted, cyan.
syn
4-OHEN-C1	intact	0	5.5	11.9	3.1	0.7
4-OHEN-A1	intact	0	5.9	14.3	1.8	-1.3
4-OHEN-G1	intact	2	3.2	4.2	-5.7	1.6
4-OHEN-C2	intact	1	4.6	11.0	3.1	2.0
4-OHEN-A2	intact	2	4.7	8.7	2.3	2.1
4-OHEN-G2	distorted	1	5.4	0.7	3.0	2.4
4-OHEN-C3	intact	0	5.3	-0.7	-2.2	-2.3
4-OHEN-A3	intact	1	6.6	15.6	1.0	1.8
4-OHEN-G3	distorted	3	5.1	-2.5	2.8	3.6
4-OHEN-C4	distorted	2	9.2	0.1	5.3	-6.0
4-OHEN-A4	intact	2	3.1	7.5	2.9	2.7
4-OHEN-G4	distorted	2	3.4	4.3	4.0	2.1
anti
4-OHEN-C1	distorted	0	22.2	4.1	5.2	8.8
4-OHEN-A1	broken	2	_g	26.3	1.4	6.2
4-OHEN-G1	broken	3	12.8	13.5	10.7	2.2
4-OHEN-C2	broken	1	19.7	15.8	3.7	-2.6
4-OHEN-A2	broken	2	22.1	38.9	4.1	9.5
4-OHEN-G2	broken	4	11.3	7.0	4.7	3.5
4-OHEN-C3	broken	3	22.6	38.4	2.2	8.2
4-OHEN-A3	broken	1	_g	32.9	4.7	6.1
4-OHEN-G3	distorted	3	12.6	26.4	7.1	2.7
4-OHEN-C4	broken	2	15.9	40.1	2.8	1.6
4-OHEN-A4	broken	0	20.9	39.8	13.4	-1.9
4-OHEN-G4	broken	4	20.8	28.5	5.4	3.2

^aData for 4-OHEN-C and A from (39, 40).

^bWatson-Crick hydrogen bonds: intact, occupancy of all > 90%; distorted, occupancy of any one 50%-90%; broken, occupancy of all 0%. Distorted or broken hydrogen bonds are at the base pair adjacent to the lesion in the direction of the equilenin ring orientation in 20 of 24 cases, excepting syn 4-OHEN-G2, G4 and C4, and anti C1; for these the disturbance is at the base pair adjacent to the lesion in the direction opposite to the equilenin ring orientation due to specific hydrogen bonding and stacking interactions (39). The unmodified duplex has all base pairs intact.

^cNumber of hydrogen bonds involving 4-OHEN base adduct with occupancy > 50% in stable time frame of trajectory (see Methods and Table S6).

^dDifference between stacking interaction energy of modified duplex and its unmodified counterpart (Table S7). Larger energies show more perturbed stacking.

^eDifference between the trajectory average bend angle of the adduct and the unmodified duplex (Table S8).

^fUsing the unmodified duplex as reference, we calculated the groove distortions of the modified duplexes as (d-d0), where d is a groove dimension of the modified duplex, and d0 is the corresponding value for the unmodified duplex (Figure S4). The groove dimension difference with the largest absolute value is shown. A negative sign indicates groove closing compared to the unmodified control.

^gStacking cannot be calculated due to the dangling end.