Table 1.
List of oligonucleotides
| Name of Oligonucleotide | Sequence (in 5′ – 3′ direction) | Application |
|---|---|---|
| Probe_norf1_fw | GTAATACGACTCACTATAGGGAGACCATCGACTATTCTTCAGTACTGTTTAC | Amplification of probe template norf1 (168 nt) for in vitro-transcription (T7 promoter is underlined) |
| Probe_norf1_rev | TTGAGATGCTACAGGACCTTATGC | |
| Pnorf1_fw | taccggtGCCTAGGGGATACCTCTCCCC | Amplification of putative norf1 promoter for ligation into pILA reporter plasmid |
| Pnorf1_rev | tggccggcCTCCGTCCCAATGGGGGAAAC | |
| nsiR6_probe_fw | GTAATACGACTCACTATAGGGAGATTACCGATCGCCGCTTCATC | Amplification of probe template nsiR6 (166 nt) for in vitro-transcription (T7 promoter is underlined) |
| nsiR6_probe_rev | TGTGTGGCGTCACCATTGAAAATG | |
| hliR1_probe_fw | GTAATACGACTCACTATAGGGAGACTCGGGAAGATTAAGACTGGTTTTG | Amplification of probe template hliR1 (135 nt) for in vitro-transcription (T7 promoter is underlined) |
| hliR1_probe_rev | ATGTCTAATTTGATTGCTGTTGCTTTC | |
| norf4_probe_fw | GTAATACGACTCACTATAGGGAGACCCCCTTTAGCAAAACTACCCATC | Amplification of probe template norf4 (116 nt) for in vitro-transcription (T7 promoter is underlined) |
| norf4_probe_rev | ATGACCGCCGATCAACTGTTG | |
| nsiR6_fw | gccaagaagtATGAGTGTTTTCCCCGCAGA | Amplification of nsiR6 generating overlaps with PpetE and 3xFLAG::3′UTR norf1::Toop |
| nsiR6_rev | tataatccatGTCGTAATAATCCCGGCTGG | |
| PpetE::hliR1_fw | gccaagaagtATGTCTAATTTGATTGCTGTTG | Amplification of hliR1 generating overlaps with PpetE and 3xFLAG::3′UTR norf1::Toop |
| 3xFlag_hliR1_rev | tataatccatCTCGGGAAGATTAAGACTGG | |
| PpetE::ssr1169_fw | gccaagaagtATGGATATTGTTAAGATCATTTGTGCGATTC | Amplification of ssr1169 generating overlaps with PpetE and 3xFLAG::3′UTR norf1::Toop |
| 3xFlag_ssr1169_rev | tataatccatACGTTCCCTGGCAATGACCC | |
| PpetE::Norf4_fw | gccaagaagtATGACCGCCGATCAACTGTT | Amplification of n orf4 generating overlaps with PpetE and 3xFLAG::3′UTR n orf1::Toop |
| 3xFlag_Norf4_rev | tataatccatACCCCCTTTAGCAAAACTAC | |
| pUC19-XbaI_PpetE_fw | gctcggtacccggggatcctctagaCTGGGCCTACTGGGCTATTC | Amplification of PpetE introducing XbaI site (underlined) + creating overlaps with pUC19 and nsiR1, hliR 1, ssr1169 or n orf4 |
| nsiR6::PpetE_rev | aaacactcatACTTCTTGGCGATTGTATCTATAGG | |
| hliR1::PpetE_rev | aattagacatACTTCTTGGCGATTGTATCTATAGG | |
| ssr1169::PpetE_rev | caatatccatACTTCTTGGCGATTGTATCTATAGG | |
| Norf4::PpetE_rev | gatcggcggtcatACTTCTTGGCGATTGTATCTATAGG | |
| 3xFlag_PstI-pUC19_rev | gccaagcttgcatgcctgcagAATAAAAAACGCCCGGCGGC | Amplification of 3xFLAG::3′UTR norf1::Toop introducing PstI site (underlined) + creating overlaps with pUC19 and nsiR1, hlirR, ssr1169 or norf4 or amplification of particular CDS associated with 3xFLAG__3′UTR norf1::Toop introducing PstI site (underlined) + creating overlaps with pUC19 and respective promoter sequence |
| nsiR6_3xFlag_fw | ttattacgacATGGATTATAAAGATCATGATGGCGATTATAAAG | |
| hliR1_3xFlag_fw | tcttcccgagATGGATTATAAAGATCATGATGGCGATTATAAAG | |
| ssr1169_3xFlag_fw | cagggaacgtATGGATTATAAAGATCATGATGGCGATTATAAAG | |
| Norf4_3xFlag_fw | taaagggggtATGGATTATAAAGATCATGATGGCGATTATAAAG | |
| CDSnsiR6::PnsiR6_fw | ataaatactcATGAGTGTTTTCCCCGCAGAAAC | |
| CDShliR1::PhliR1_fw | aaattaactaaATGTCTAATTTGATTGCTGTTGCTTTCTG | |
| CDSNorf4::PNorf4_fw | aatttttaccATGACCGCCGATCAACTGTTG | |
| CDSssr1169::Pssr1169_fw | gagtgaactaATGGATATTGTTAAGATCATTTGTGCGATTC | |
| pUC19::PnsiR6_fw | gctcggtacccggggatcctctagaATCGCCGTATTACACCTCTG | Amplification of PnsiR6 introducing XbaI site (underlined) + generating overlaps with pUC19 and nsiR6. |
| PnsiR6::CDSnsiR6_rev | aaacactcatGAGTATTTATTCCTAGTGAATGAATTAGAAG | |
| pUC19::PhliR1_fw | gctcggtacccggggatcctctagaGGAGTTTACAGCGAGATTTG | Amplification of PhliR1 introducing XbaI site (underlined) + generating overlaps with pUC19 and hliR1. |
| PhliR::CDShliR1_rev | aattagacatTTAGTTAATTTTTGTAACGGGAG | |
| pUC19::PNorf4_fw | gctcggtacccggggatcctctagaAGGTGATGATTATGAGCCGTC | Amplification of Pnorf4 introducing XbaI site (underlined) + generating overlaps with pUC19 and norf4. |
| PNorf4::CDSNorf4_rev | gatcggcggtcatGGTAAAAATTCCACTAATTCAAAAAAC | |
| pUC19::Pssr1169_fw | gctcggtacccggggatcctctagaCGAGTAGCCAGCCAAAGCAG | Amplification of Pssr1169 introducing XbaI site (underlined) + generating overlaps with pUC19 and ssr1169. |
| Pssr1169::CDSssr1169_rev | caatatccatTAGTTCACTCCAATATGTCGGGATAATTAG |