Table 1.

Oligonucleotide duplexes and yields of hairpin DNA products in BfiI reactions

Duplex	Oligonucleotide duplex sequence*	Max. hairpin yield, %
14/15	5′-AGCACTGGGCTGC–T-3′	0
	3′-TCGTGACCCGACGpAC-5′
25C/15	5′-AGCACTGGGCTGC–TGAACTAGTTCA-3′	38 ± 2
	3′-TCGTGACCCGACGpAC-5′
25CddA/15†	5′-AGCACTGGGCTGC–TGAACTAGTTCddA-3′	0
	3′-TCGTGACCCGACGpAC-5′
15/15	5′-AGCACTGGGCTGC–TG-3′	0
	3′-TCGTGACCCGACGpAC-5′
16/15	5′-AGCACTGGGCTGC–TGA-3′	5.5 ± 1
	3′-TCGTGACCCGACGpAC-5′
17/15	5′-AGCACTGGGCTGC–TGAG-3′	14 ± 1
	3′-TCGTGACCCGACGpAC-5′
25/15	5′-AGCACTGGGCTGC–TGAACTGTGCTG-3′	28 ± 3
	3′-TCGTGACCCGACGpAC-5′
29/15	5′-AGCACTGGGCTGC–TGAACTGTGCTGCGGC-3′	1.4 ± 0.5
	3′-TCGTGACCCGACGpAC-5′
25C/15(S)Rp‡	5′-AGCACTGGGCTGC–TGAACTAGTTCA-3′	36 ± 5
	3′-TCGTGACCCGACGsAC-5′
25C/15(S)Sp§	5′-AGCACTGGGCTGC-TGAACTAGTTCA-3′	37 ± 5
	3′-TCGTGACCCGACGsAC-5′

*The BfiI recognition sequence is underlined, and the scissile phosphodiester bond in the bottom DNA strand is noted as p. Unless noted otherwise, all duplexes carried a radiolabel at the 3′ terminus of the bottom strand.

^†The 3′-terminal nucleoside of the top strand of 25CddA/15 is dideoxyadenosine (ddA).

^‡The 25C/15(S)Rp duplex contains an R_p–PTO linkage at the scissile position of the bottom strand (marked s).

^§The 25C/15(S)Sp duplex contains an S_p–PTO linkage at the scissile position of the bottom strand (marked s).