Table 1.

DNA substrates

Name	Sequence
Uracil hairpin (U-hp)	5′-(HEX) GAC TAA UAA TGA CTG CGG TTA CGC AGT CAT TGT TAG TCT*T*T*T-3′
AP·G	5′-(HEX) GCT ATG GAC TAA (THF)AA TGA CTG CGT G-3′
	CGA TAC CTG ATT G TT ACT GAC GCA C-5′
C·G	5′-(HEX) GCT ATG GAC TAA CAA TGA CTG CGT G-3′
	CGA TAC CTG ATT GTT ACT GAC GCA C-5′
50-U	5′-(HEX) CGT GTA TGA CAT CTA ACT ATU ATA GCG CTC ATC GTC ATC GTC ATC CTC GGC ACC GT-3′
	3′-GCA CAT ACT GTA GAT TGA TAG TAT CGC GAG TAG CAG TAG CAG TAG GAG CCG TGG CA-5′
50-PO4a	5′-(HEX) CGT GTA TGA CAT CTA ACT AT(PO4) ATA GCG CTC ATC GTC ATC GTC ATC CTC GGC ACC GT-3′
	3′-GCA CAT ACT GTA GAT TGA TA G TAT CGC GAG TAG CAG TAG CAG TAG GAG CCG TGG CA-5′
20-PO4	5′-(HEX) CGT GTA TGA CAT CTA ACT AT(PO4)
	3′-GCA CAT ACT GTA GAT TGA TA G TAT CGC GAG TAG CAG TAG CAG TAG GAG CCG TGG CA-5′
20-OH	5′-(HEX) CGT GTA TGA CAT CTA ACT AT
	3′-GCA CAT ACT GTA GAT TGA TAG TAT CGC GAG TAG CAG TAG CAG TAG GAG CCG TGG CA-5′
ss20-OH	5′-(HEX) CGT GTA TGA CAT CTA ACT AT-3′
ss20-PO4	5′-(HEX) CGT GTA TGA CAT CTA ACT AT (PO4)-3′

THF is a tetrahydrofuran analogue; * is a methyl phosphonate linkage; U is deoxyuracil.

^aSubstrate 50-PO₄ was generated by enzymatic digestion of 50-U; see phosphatase assay for details.