. 2011 Jul 19;39(20):8844–8856. doi: 10.1093/nar/gkr588

Table 1.

Oligonucleotide substrates

Duplex	Sequence^a	Specification
HP	`5′-CTTCGCAGTACGCCpGGGCAATAACGCACGT\`	A hairpin substrate with a single BcnI recognition sequence.^b
HP	`3′-GAAGCGTCATGCGGCpCCGTTATTGCGTGAT/`
30/30	`5′-CTTCGCAGTACGCCpGGGCAATAACGCACGT-3′`	Same as HP, but lacks the hairpin loop. Was used as unlabeled trap DNA.
30/30	`3′-GAAGCGTCATGCGGCpCCGTTATTGCGTGCA-5′`
G-nick	`5′-CTTCGCAGTACGCCGGGCAATAACGCACGT-3′`	As 30/30, except for the nick in the scissile position of the G-strand (designated by a gap).^c
G-nick	`3′-GAAGCGTCATGCGGCpCCGTTATTGCGTGCA-5′`
C-nick	`5′-CTTCGCAGTACGCCpGGGCAATAACGCACGT-3′`	As 30/30, except for the nick in the scissile position of the C-strand (designated by a gap).^c
C-nick	`3′-GAAGCGTCATGCGGCCCGTTATTGCGTGCA-5′`
GG	`/TAGCAGTACGCC*GGGCAACGCCpGGGCAATAACGCA-3′`	A hairpin substrate that carries two BcnI sites in direct repeat orientation. The internal ³³P label is designated by *.
GG	`\TGCGTCATGCGGCpCCGTTGCGGCpCCGTTATTGCGT-5′`

^aThe BcnI recognition sequences are underlined; scissile positions are designated by ‘p’.

^bThe HP substrate carried a radiolabel either at the 5′ or the 3′ terminus.

^cThe G-nick and the C-nick substrates carried a radiolabel at the 5′ terminus of the 30 nt strand and a 5′-terminal phosphate at the position of the nick.