Table 1. Oligonucleotide substrates.
| Duplex | Sequence a | Specification |
| 16-M | 5′-CGTAGCMTGGTCGATC-3′ | |
| 3′-GCATCGGACCAGCTAG-5′ | A short cognate LpnPI oligoduplex | |
| 16-C | 5′-CGTAGCCTGGTCGATC-3′ | |
| 3′-GCATCGGACCAGCTAG-5′ | As 16-M but 5mC is replaced with an unmodified cytosine | |
| 16-P | 5′-CGTAGCPTGGTCGATC-3′ | |
| 3′-GCATCGGACCAGCTAG-5′ | As 16-M but 5mC is replaced with a pyrrolocytosine | |
| 16-T | 5′-CGTAGCTTGGTCGATC-3′ | |
| 3′-GCATCGGACCAGCTAG-5′ | As 16-M but 5mC is replaced with a thymine | |
| 16-T-N | 5′-CGTAGATCTTACGATC-3′ | |
| 3′-GCATCTGGAATGCTAG-5′ | Noncognate LpnPI oligoduplex with a T-G mismatch. | |
| 30-M | 5′-CCGTAGCMTGGTCGATCCTAGCTGGTCGCC-3′ | |
| 3′-GGCATCGGACCAGCTAGGATCGACCAGCGG-5′ | An extended cognate LpnPI oligoduplex | |
| 30-C | 5′-CCGTAGCCTGGTCGATCCTAGCTGGTCGCC-3′ | |
| 3′-GGCATCGGACCAGCTAGGATCGACCAGCGG-5′ | As 30-M but 5mC is replaced with an unmodified cytosine | |
| 30-P | 5′-CCGTAGCPTGGTCGATCCTAGCTGGTCGCC-3′ | |
| 3′-GGCATCGGACCAGCTAGGATCGACCAGCGG-5′ | As 30-M but 5mC is replaced with a pyrrolocytosine | |
| 30-T | 5′-CCGTAGCTTGGTCGATCCTAGCTGGTCGCC-3′ | |
| 3′-GGCATCGGACCAGCTAGGATCGACCAGCGG-5′ | As 30-M but 5mC is replaced with a thymine | |
| 39-H/H | 5′-CGACGATAHTTACCGGATAAGGCGCAATTAGATTACTTC-3′ | |
| 3′-GCTGCTATGAATGGCCTATTCCGCGTTAATHTAATGAAG-5′ | Optimal YkrI and BmeDI substrate with two 5hmC-G base pairs | |
| 39-M/H | 5′-CGACGATAMTTACCGGATAAGGCGCAATTAGATTACTTC-3′ | |
| 3′-GCTGCTATGAATGGCCTATTCCGCGTTAATHTAATGAAG-5′ | As 39-H/H but one 5hmC is replaced with a 5-methylcytosine | |
| 39-C/H | 5′-CGACGATACTTACCGGATAAGGCGCAATTAGATTACTTC-3′ | |
| 3′-GCTGCTATGAATGGCCTATTCCGCGTTAATHTAATGAAG-5′ | As 39-H/H but one 5hmC is replaced with an unmodified cytosine | |
| 39-P/H | 5′-CGACGATAPTTACCGGATAAGGCGCAATTAGATTACTTC-3′ | |
| 3′-GCTGCTATGAATGGCCTATTCCGCGTTAATHTAATGAAG-5′ | As 39-H/H but one 5hmC is replaced with a pyrrolocytosine | |
| 39-T/H | 5′-CGACGATATTTACCGGATAAGGCGCAATTAGATTACTTC-3′ | |
| 3′-GCTGCTATGAATGGCCTATTCCGCGTTAATHTAATGAAG-5′ | As 39-H/H but one 5hmC is replaced with a thymine | |
| 39-H | 5′-CGACGATATTTACCGGATAAGGCGCAATTAGATTACTTC-3′ | |
| 3′-GCTGCTATAAATGGCCTATTCCGCGTTAATHTAATGAAG-5′ | As 39-H/H but one 5hmC-G base pair is replaced with a T-A base pair | |
| 39-T | 5′-CGACGATATTTACCGGATAAGGCGCAATTAAATTACTTC-3′ | |
| 3′-GCTGCTATGAATGGCCTATTCCGCGTTAATTTAATGAAG-5′ | As 39-T/H but the 5hmC-G base pair is replaced with a T-A base pair | |
| 31-C | 5′-TGACCCACGCTCGCCCGGCGACACATTACGT-3′ | |
| 3′-ACTGGGTGCGAGCGGGCCGCTGTGTAATGCA-5′ | Cognate Ecl18kI oligoduplex with a C-G central base pair | |
| 31-M | 5′-TGACCCACGCTCGCCMGGCGACACATTACGT-3′ | |
| 3′-ACTGGGTGCGAGCGGGCCGCTGTGTAATGCA-5′ | As 31-C but with a central 5mC-G base pair |
a
M designates 5-methylcytosine (5mC), H designates 5-hydroxymethylcytosine (5hmC), P designates pyrrolocytosine. Modified bases and mismatched base pairs are shown in boldface, recognition sequences are underlined.