. Author manuscript; available in PMC: 2015 Dec 30.

Published in final edited form as: Chem Res Toxicol. 2005 Mar;18(3):441–456. doi: 10.1021/tx049786v

Table 2.

Distances and Occupancies for C1′–C1′ and Pα–O3′

model	dNTP	C1′–C1′ distance (Å)^a	C1′–C1′ occupancy (%)^b	Pα–O3′ distance (Å)^a	Pα–O3′ occupancy (%)^c
control	dTTP	10.8 ± 0.3	100.0	3.5 ± 0.1	73.3
intercalation	dTTP	8.9 ± 0.3	1.1	5.7 ± 0.9	3.7
	dCTP	8.7 ± 0.4	0.6	5.6 ± 0.6	0.05
	dATP	9.6 ± 0.3	40.7	4.0 ± 0.6	7.7
	syn-dATP	8.8 ± 0.4	3.0	6.5 ± 0.5	0.0
	dGTP	10.1 ± 0.4	88.9	4.1 ± 1.0	39.5
	syn-dGTP	9.9 ± 0.5	75.1	6.7 ± 0.6	0.0
major groove type I	dTTP	10.8 ± 0.2	100.0	3.7 ± 0.1	9.4
	dCTP	11.8 ± 0.4	71.5	4.8 ± 0.3	0.0
	dATP	11.5 ± 0.4	91.5	6.5 ± 0.7	0.0
	syn-dATP	11.1 ± 0.4	99.8	3.2 ± 0.1	99.8
	dGTP	12.3 ± 0.2	8.6	5.5 ± 0.5	0.8
	syn-dGTP	11.1 ± 0.3	99.8	3.1 ± 0.1	100.0
–1 deletion	dGTP	10.7 ± 0.2	100.0	5.7 ± 0.8	2.8

Average values and standard deviations are provided. C1′–C1′ distances are for residues of the nascent base pair, and Pα–O3′ distances are between Pα of dNTP and O3′ of the primer terminus.

Criterion for C1′–C1′ distance occupancy: within 10.8 ± 1.2 Å.

Criterion for Pα–O3′ distance occupancy: ≤ 3.6 Å.