Table 1.
Oligonucleotides used
| Purpose and DNA oligonucleotide | Sequence |
|---|---|
| Probes | |
| Ser AGA ACL | CCAATGGATTTCTAGTCCATCGC |
| Ser AGA body | GCAGGATTCGAACCTGCGCGG |
| Ser CGA ACL | CCCATTGGATTTCGAGTCCAACGCCT |
| Ser CGA body | AGCAGGATTCGACCTGCGCGGGG |
| Ser UGA ACL | CCCATTGGATTTCAAGTCCAACGC |
| Ser UGA body | GCAGGATTCGAACCTGCGCGGG |
| Leu CAA ACL | CCATTCAGATTTTGAGACTGATGCG |
| Leu CAA body | CCTCTGAGGCTTGAACTCAG |
| Leu UAA-1 ACL | GATTATAAAATTTTAAGTTTTATGC |
| Leu UAA-1 body | GTTAAGAAGAGGAGTTGAACC |
| Leu UAA-2 ACL | TTATAAAGTTTTAAGTCTTATG |
| Leu UAA-2 body | GTTAATGTGAGGAGTTGTACC |
| Sec ACL | GCTACAGGTTTGAAGCCTGCACC |
| Sec body | CAAAGGTGGAATTGAACCACTC |
| Sec-3 body | CACAAAGGGACTCAAACC |
| mt Ser UGA ACL | CAAAGCTGGTTTCAAGCCAACCCC |
| mt Ser UGA body | AAGGAAGGAATCGAACCCCCC |
| mt Trp UCA ACL | CTGAGGGCTTTGAAGGCTCTTGG |
| mt Trp UCA body | GAAATTAAGTATTGCAACTTAC |
| mt Phe GAA ACL | GTCTAAACATTTTCAGTGTATTGC |
| mt Phe GAA body | GTGTTTATGGGGTGATGTGATGTGAGCC |
| mt Leu UUA ACL | GACTGTAAAGTTTTAAGTTTTATGC |
| mt Leu UUA body | GTTAAGAAGAGGAATTGAACCTC |
| mt Tyr GUA ACL | TCTTTAGATTTACAGTCCAATGC |
| mt Tyr GUA body | GGTAAAAAGAGGCCTAACCCCTG |
| mt Cys GCA ACL | TCTTCGAATTTGCAATTCAATATG |
| mt Cys GCA body | AGCCCCGGCAGGTTTGAAGCT |
| Antisense to eliminate tRNAs with RNase H | |
| mt Ser RNase H | GGCAAAAAAGGAAGGAATCGAACCCCCCAAAG |
| mt Trp RNase H | GGCAGAAATTAAGTATTGCAACTTACTG |
| mt Phe RNase H | GGTGTTTATGGGGTGATGTGAGCCCGTCTA |
| mt Leu RNase H | GGTGTTAAGAAGAGGAATTGAACCTCTGACTG |
| mt Tyr RNase H | GGTGGTAAAAAGAGGCCTAACCCCTGTCT |
| mt Cys RNase H | GGAAGCCCCGGCAGGTTTGAAGCTGCTCT |
| cyto-Leu CAA RNase H | CCCCTCTGAGGCTTGAACTCAGGACCATTC |
| cyto-Leu UAA-1 RNase H | AGAAGAGGAGTTGAACCTCTGATTATAAA |
| cyto-Leu UAA-2 RNase H | TGATTATAAAGTTTTAAGTCTTATGCAA |
| cyto-Cys RNase H | GGGGGCACCTGGATTTGAATCAGGGACCTC |
| Sec-1 AAS/RNase H | GCCCGAAAGGTGGAATTG |
| Sec-2 AAS/RNase H | CCTACAAAGGTGGAATTG |
| Subcloning | |
| TRIT1 clone NdeI forward primer | AATCGATA CAT ATG GCG TCC GTG GCG GCT GC |
| TRIT1 clone XhoI reverse primer | TACGTACG CTC GAG TTA AAC GCT GCA TTT CAG C |
| In vitro modification oligonucleotides | |
| Ser AGA RNA | rG rArUrG rGrArC rUrArG rArArA rUrCrC rArUrC |
| Ser CGA RNA | rG rUrUrG rGrArC rUrCrG rArArA rUrCrC rArA rC |
| Ser UGA RNA | rG rArUrG rGrArC rUrUrG rArArA rUrCrC rArUrC |
| Leu CAA RNA | rG rUrCrArG rUrCrU rCrArA rArArU rCrUrGrA rC |
| Leu UAA-1 RNA | rG rUrArArArA rCrUrU rArArArA rUrUrUrUrArC |
| Leu UAA-2 RNA | rG rUArA rGrArC rUrUrA rArArA rCrUrU rUrArC |
| Cys GCA RNA | rG rUrUrU rGrArC rUrGrC rArArA rUrCrA rArGrC |
| Sec UCA RNA | rG rUrGrC rArGrG rCrUrU rCrArA rArCrC rUrGrU rArC |