Table 2.

Biophysical properties and RNase H activity of S-ONs

ON	Sequence	Base modifications	krel on*	krel off*	Krel†	RNase H, cleavage %‡
9	TGG CTC TCC TGC GCC	none	1.0	1.0	1	21.7
8	UGG CUC UCCUGCGCC	pC, pU	2.5	0.60	4.2	4.9
10	TGG CTC TCP TGC GCC	P	0.9	1.1	0.81	9.1
4	TGG CTC TCX TGC GCC	G-clamp	1.7	0.77	2.2	17.4

Boldface indicates the position of the substituted heterocycle modification. All eleven pyrimidines in ON8 are C5-propynyl-modified. S-ON base modifications are shown in Fig. 1. The S-ONs contain C5-propynyl (pC, pU), phenoxazine (P) and G-clamp (X). All linkages are phosphorothioate. T, thymidine; G, 2′-deoxyguanosine; C, 2′-deoxy-5′-methylcytidine. 

^*The relative association rates (k_rel on and k_rel off) were determined as described in Materials and Methods. The relative rates have been normalized to the value for the unmodified S-ON (ON9). For k_rel on, a value >1 indicates that the S-ON associates faster than the unmodified S-ON control. For k_rel off, a value <1 indicates that the S-ON dissociates slower than the unmodified S-ON control. Each of the above experiments were repeated in duplicate, and similar results were obtained. 

^†K_rel = k_rel on/k_rel off. 

^‡The percent RNA cleavage by RNase H in HeLa nuclear extracts after 5 min at 37°C.