Table 1.
Oligoribonucleotides and PNA used in this study
| A: Oligoribonucleotides used as PNA binding target for thermal denaturation experiments | |
| RNA-I-wt: | 5′AAAAGAAAAGGGG3′ |
| RNA-I-mut: | 5′AAAAGAAAAAGGA3′ |
| RNA-II-wt: | 5′AGAAAAGGGGGGA3′ |
| RNA-II-mut: | 5′AGAAAAAGAGAGA3′ |
| B: Oligoribonucleotides used as PNA binding target for gel shift assays | |
| RNA-III-wt: | 5′UUAAAAGAAAAGGGGGGAU3′ |
| RNA-III-mut: | 5′AUAAAAGAAAAAGGAGGAU3′ |
| C: PNAas used in this study | |
| 13mer-I PNA: | NH2-CCCCTTTTCTTTT-Lys |
| 13mer-II PNA: | NH2-TCCCCCCTTTTCT-Lys |
| 13mer-I-Acr PNA: | Acr-eg1-CCCCTTTTCTTTT-Lysb |
| 9mer PNA: | NH2-TTTTCTTTT-Lys |
| 9mer-Acr PNA: | Acr-AEEA-TTTTCTTTT-Lysc |
| 9mer-bis-PNA: | NH2-TTTTCTTTT-AEEA-TTTTCTTTT-Lysc |
| 11mer-bis-PNA: | NH2-CCTTTTCTTTT-AEEA-TTTTCTTTTCC-Lysc |
| 13mer-scr PNA: | NH2-TTTTCCTCTCCCT-Lys |
| D: ODNs used for RNAse H cleavage | |
| 15mer-PPT: | 5′ TCTTTTAAAATTGTG3′ |
| 15mer-PPT-I: | 5′ AATTTTCTTTAATTC3′ |
| 15mer-PPT-II: | 5′ TTATTCTTTAGTTTG3′ |
aPNA base sequences are written from N to C terminus.
beg1, 8-amino-3, 6 dioxaoctanoic acid.
cAEEA, 2-(2aminoethoxy) ethoxy acetic acid.