Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

Table 3

A comparison of the local base-pair parameters at the modified pairs, calculated with the program 3DNA [20].

	Pair	fUA^1	fUA^2	fUA^3	fUA^4	fUG^1	fUG^2	fUG^3	Ave	Unm
Shear (Å)	fU8:R	0.01	−0.03	−0.05	−0.08	−2.00	−2.24	−2.19	−0.94	−0.11
	R:fU20	0.05	0.08	−0.04	−0.01	1.90	−2.08	2.15	0.29	−0.04
Stretch (Å)	fU8:R	−0.19	−0.13	−0.08	−0.10	0.15	0.00	0.08	−0.04	−0.12
	R:fU20	−0.10	−0.11	−0.16	−0.16	0.13	−0.58	0.10	−0.13	−0.11
Stagger (Å)	fU8:R	0.10	0.11	−0.06	0.08	−0.33	−0.08	0.03	−0.02	−0.00
	R:fU20	0.09	0.00	0.00	0.10	−0.06	0.10	−0.05	0.03	0.01
Buckle (°)	fU8:R	−6.04	−4.89	−2.68	−4.97	−5.62	−10.56	−9.96	−6.39	−1.56
	R:fU20	8.11	6.02	9.91	9.34	6.78	8.68	4.50	7.62	4.72
Propeller (°)	fU8:R	−12.4	−12.4	−12.5	−11.9	−9.1	−16.3	−13.3	−12.6	−16.4
	R:fU20	−14.3	−14.5	−15.2	−15.3	−18.8	−14.6	−13.9	−15.2	−15.3
C^1'⋯C^1'	fU8:R	10.4	10.5	10.4	10.4	11.0	11.2	11.0	10.5(WC)	10.5
(Å)	R:fU20	10.5	10.6	10.3	10.4	11.1	10.6	11.1	11.1(rw)	10.5

R: a purine residue, A or G, Ave: average, Unm: unmodified duplex [14], WC: Watson-Crick type and rw: reversed wobble.