Table 2.

Direct and indirect base pair opening induced by DNA-DNA interactions. The star denotes the cytosine that makes an hydrogen bond with the inserted phosphate group.The # denotes a residue from a symmetry related molecule. The base-pairs represented in red are partially disrupted.

	Space group	Resol.	Sequence	Structural alteration
Base unstacking
Bdjb77 (286D)	P31	2.5	5'-CC I I I CCCGG	High propeller twist and buckle values (from C6-I15 to C8 I13) in front of inserted phosphate groups (Table 1)
			3'-GGCCC I I I CC
Bd0015 (1QC1)	H 3	2.5	5'-CCGCCGGCGG	Alterations of base stacking along the whole structure (Table 1)
			3'-GGCGGCCGCC
Bd0084 (1ZFG)	P31	1.75	5'-CCGAGCTCGG	Alterations of base stacking in front of the inserted phosphate groups (Table 1)
			3'-GGCTCGAGCC
Direct base-pair opening
Bd0022 (1QP5)	H 3	2.6	* *	C3-G17(#): N4-O1P: 2.4 Å
				C21-G17(#): N4-O1P: 3.3 Å
				C18-C20(#): N4-O1P: 2.9 Å
			* *	Shift of the base pairing in the major groove (Figure 5) from
Bdl035 (330D)	H 3	2.7	5'-ACCGCCGGCGCC	Normal base-pairing
			3'-TGGCGGCCGCGG
Bd0076 (1ZEW)	C2	2.25		C12-G7(#): N4-O1P: 2.7 Å
				: N4-O6: 4.0 Å
				N3-N1: 3.3 Å
				O2-N2: 2.7 Å
				: O4-N6: 3.6 Å
			*	N3-N1: 3.6 Å
				A18-T15(#) N6-O1P: 6.9Å
				: N6-O4 : 4.0 Å
				N1-N3: 3.7 Å
Bd0028 (1ZFH)	C2	2.5	5'-CCGCTAGCGG	Normal base-pairing
			3'-GGCGATCGCC
Bd0021 (1CW9)	P212121	1.55	*	C6-G10(#): N4-O1P: 3 Å
				: N4-O6: 7.0 Å
			3'-GGTCCGGACC	(2 mol/au: open and closed form)
Indirect base-pair opening
Bdf062 (206D)	P6122	2.5	*	C1-C8(#): N4-O1P: 3.3 Å
				C10-A9(#): C6-O1P: 2.9 Å
				C5-O2P: 3.3 Å
				: O4-N6: 4.7 Å
				O2-N6: 2.9 Å
				Unstacking C1/G2/G3
Ud0029 (1P4Z)	P6122	2	*	C7-A6(#): N4-O1P: 3.0 Å
				N4-O6: 3.3 Å
				N6-O4: 3.8 Å
			*	N1-N3: 3.5 Å
Bd0068 (1S1K)	P6122	1.9	5'-CCMGTACTGG	Normal base-pairing
			3'-GGTCATGMCC
			M=1AP