Table 1.
Oligonucleotide sequences used in the study
| Oligo | Figure | Sequence |
|---|---|---|
| 70 nucleotide minicircle DNA | Figs 1, 2, 3 and 6, and Appendix Figs S1, S2 and S5 |
5′ CACCATATCCTCGACCATCCCCAATATGGTCCATCAACCCTTCACCTCACTTCACTCCACTATACC ACTC 3′ |
| Primer for the 70 nucleotide minicircle DNA | Figs 1, 2, 3 and 6, and Appendix Figs S1, S2 and S5 | 5′ TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGTGGTATAGTGGAGTGAAGTGAGGTGAAGGGTTGATGGACCATATTGGGGATGGTCGAGGATATGGTG 3′ |
| Primer 6236 for M13 ssDNA | Fig 5 and Appendix Fig S1F | 5′ GACTCTAGAGGATCCCCGGGTACCGAGCTC 3′ |
| Matched primer 25‐mer | Appendix Fig S4 | 5′ 6‐FAM/TGGTTAGTGGAAGAGATTCACAAAC 3′ |
| Template 55‐mer | Appendix Fig S4 | 5′ ACTTATCACACATTCTTCTCATTAACTTGTGTTTGTGAATCTCTTCCACTAACCA 3′ |
| Matched Primer 35‐mer | Fig 4 and Appendix Fig S3 | 5′ FAM/AGGAGTGCGCTGGTTAGTGGAAGAGATTCACAAAC 3′ |
| Template 65‐mer | Fig 4 and Appendix Fig S3 | 5′ ACTTATCACACATTCTTCTCATTAACTTGTGTTTGTGAATCTCTTCCACTAACCAGCGCACTCCT 3′ |
| Abasic Template 55‐mer | Appendix Fig S4C | 5′ ACTTATCACACATTCTTCTCATTAACTTG/Abasic/GTTTGTGAATCTCTTCCACTAACCA 3′ |
| Mismatched Primer 35‐mer | Fig 4 and Appendix Fig S3 | 5′ FAM/AGGAGTGCGCTGGTTAGTGGAAGAGATTCACAAAG 3′ |
| Mismatched Primer 35‐mer with Phosphorothioate linkage | Appendix Fig S2A | 5′ FAM/AGGAGTGCGCTGGTTAGTGGAAGAGATTCACAAA*G 3′ |
| *Phosphorothioate linkage | ||
| Trap 1 | Fig 4 and Appendix Figs S2 and S3 | 5′ AGGAGTGCGCTGGTTAGTGGAAGAGATTCACAAAC 3′ |
| Matched Primer 35‐mer with 3′dideoxy end | Fig 1F and Appendix Fig S1C | 5′ AGGAGTGCGCAGGAAAGAGGAAGAGAAACACAAAddC 3′ |
| Matched template 68‐mer | Fig 1F and Appendix Fig S1C | 5′ CATTATCACACATTCGTCTCATTGACTTGTCTGGTTTGTGTTTCTCTTCCTCTTTCCTGCGCACTCCT 3′ |
| Fork DNA 1 | Appendix Fig S2Bi and Bii |
5′ BHQ1/GACATGACTGACGAGAGAGTCTTGTGATGCTCCTACGTAGGCTACGCTATGTCGTCA AGTTCACACTGTTACTAG 3′ |
| Fork DNA 2 | Appendix Fig S2Bi and Bii |
5′ TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTACGTAGGAGCATCACAAGACTCTCTCGTCAG TCATGTC/FAM 3′ |