Table 1. Oligonucleotides used in this study.
F denotes synthetic abasic site analog tetrahydrofuran.
| DNA/DNA, DNA/RNA, ssDNA, ssRNA
| |
|---|---|
| Name | Sequence (5′-3′) |
| 42F | CCGCTGAATTGCACCCTCGAFCTAGGTCGATGATCCTAAGCA |
| 42bubbleComp | TGCTTAGGATCATCGAGGATCGAGCTCGGTGCAATTCAGCGG |
| 42comp | TGCTTAGGATCATCGACCTAGGTCGAGGGTGCAATTCAGCGG |
| 18DNA | TCGACCTAGATCGAGGGT |
| 18RNA | rUrCrGrArCrCrUrArGrArUrCrGrArGrGrGrU |
| 18RNAfor54comp | rUrGrGrGrArGrCrUrUrGrArUrCrCrArGrCrU |
| 54Fendbubble18 | CCGCTGCCGCTGAATTGCFCCCTCGATCTAGGTCGATGATCCTAAGCATAAGCA |
| 54Fcenterbubble18 | CCGCTGCCGCTGAATTGCACCCTCGAFCTAGGTCGATGATCCTAAGCATAAGCA |
| 54bubble18comp | TGCTTATGCTTAGGATCAAGCTGGATCAAGCTCCCAGCAATTCAGCGGCAGCGG |
| 26FDNA | AATTCACCGGTACGFACTAGAATTCG |
| 26FRNA | rArArUrUrCrArCrCrGrGrUrArCrGFrArCrUrArGrArArUrUrCrG |
| 34FDNA | CTGCAGCTGATGCGCFGTACGGATCCCCGGGTAC |
| 34FRNA | rCrUrGrCrArGrCrUrGrArUrGrCrGrCFrGrUrArCrGrGrArUrCrCrCrCrGrGrGrUrArC |
| Sequence Context
| |
| Name | Sequence (5′-3′) |
|
| |
| GFA | AATTCACCGGTACGFACTAGAATTCG |
| GFA-C | CGAATTCTAGTCCGTACCGGTGAATT |
| GFA-G | CGAATTCTAGTGCGTACCGGTGAATT |
| CFT | AATTCACCGGTACCFTCTAGAATTCG |
| CFT-C | CGAATTCTAGACGGTACCGGTGAATT |
| CFT-G | CGAATTCTAGAGGGTACCGGTGAATT |
| GFT | AATTCACCGGTACGFTCTAGAATTCG |
| GFT-C | CGAATTCTAGACCGTACCGGTGAATT |
| GFT-G | CGAATTCTAGAGCGTACCGGTGAATT |
| CFA | AATTCACCGGTACCFACTAGAATTCG |
| CFA-C | CGAATTCTAGTCGGTACCGGTGAATT |
| CFA-G | CGAATTCTAGTGGGTACCGGTGAATT |