TABLE 1.

Sequences of partial duplex substrates and single-stranded oligonucleotides

RNA strand is shown in lowercase letters. Uppercase letters indicate DNA strand.

Substrate	Use	Oligonucleotide sequence
10T/10T-16bp DNA:DNA forked duplex	Figs. 1, 2, and 9	5′-(T)10CGCTGATGTCGCCTGG-3′
		3′-(T)10GCGACTACAGCGGACC-5′
10U/10T-r16bp RNA:DNA forked duplex	Figs. 1, 2, and 9	5′-(T)10CGCTGATGTCGCCTGG-3′
		3′-(u)10gcgacuacagcggacc-5′
10T/20T-20bp DNA:DNA forked duplex	Figs. 1, 2, 3, 4a, 5a, 7, and 8	5′-(T)20GCACTCGGATCACCATGGCG-3′
		3′-(T)10CGTGAGCCTAGTGGTACCGC-5′
10U/20T-r20bp RNA:DNA forked duplex	Figs. 1, 2, 3, 4a, 5a, 7, and 8	5′-(T)20GCACTCGGATCACCATGGCG-3′
		3′-(u)10cgugagccuagugguaccgc-5′
20T-20bp DNA:DNA tailed duplex	Figs. 4a, 5a, 6, 7, and 8	5′-(T)20GCACTCGGATCACCATGGCG-3′
		3′-CGTGAGCCTAGTGGTACCGC-5′
20T-r20bp RNA:DNA tailed duplex	Figs. 4a, 5a, 6, 7, and 8	5′-(T)20GCACTCGGATCACCATGGCG-3′
		3′-cgugagccuagugguaccgc-5′
20T-16bp DNA:DNA tailed duplex	Fig. 6	5′-(T)20CGCTGATGTCGCCTGG-3′
		3′-GCGACTACAGCGGACC-5′
20T-r16bp RNA:DNA tailed duplex	Fig. 6	5′-(T)20CGCTGATGTCGCCTGG-3′
		3′-gcgacuacagcggacc-5′
Chimera fork I (10T/20T-r20bp forked duplex)	Fig. 3	5′-(T)20GCACTCGGATCACCATGGCG-3′
		3′-(T)10cgugagccuagugguaccgc-5′
Chimera fork II (10U/20T-20bp forked duplex)	Fig. 3	5′-(T)20GCACTCGGATCACCATGGCG-3′
		3′-(u)10CGTGAGCCTAGTGGTACCGC-5′
ssT50	Fig. 7	5′-(T)50-3′
14T/14T-24bp DNA:DNA forked duplex	Figs. 1 and 2	5′-(T)14CGCTGATGTCGCCTGGTACGTCGC-3′
		3′-(T)14GCGACTACAGCGGACCATGCAGCG-5′
14U/14T-24bp RNA:DNA forked duplex	Figs. 1 and 2	5′-(T)14CGCTGATGTCGCCTGGTACGTCGC-3′
		3′-(u)14gcgacuacagcggaccaugcagcg-5′

^a In Figs. 4 and 5, the 20-bp duplex substrate was used with a 5′-FAM label on the loading strand.