Table 1.
Overview of LAMP- and Hinge-primer for detection of PSTVd and beta-gal (E.coli).
| Locus: Potato Spindle Tuber Viroid (NC_002030.1) | |
|---|---|
| LAMP primer | Primer sequence (5′ – 3′) |
| F3 | AAAAAGGACGGTGGGGAG |
| B3 | CCCCGAAGCAAGTAAGATAG |
| FIP (F1 + F2) | GGAAGGACACCCGAAGAAAGG-GCCGACAGGAGTAATTCC |
| BIP (B1 + B2) | GCTGTCGCTTCGGCTACTAC-AGAAAAAGCGGTTCTCGG |
| Lf | GGTGAAAACCCTGTTTCGG |
| Lr | CGGTGGAAACAACTGAAGC |
| Hinge-primer | |
| PSTVd-um-HF | GGAAGGACACCCGAAGAAAGG-CCGAAACAGGGTTTTCACC |
| PSTVd-um-HR | GCTGTCGCTTCGGCTAC-TTCAGTTGTTTCCACCG |
| PSTVd-ab-HF | GGAAGGACACCCGAAGAAAGG[dSpacer]CCGAAACAGGGTTTTCACC |
| PSTVd-ab-HR | GCTGTCGCTTCGGCTAC[dSpacer]TTCAGTTGTTTCCACCG |
| PSTVd-HEG-HF | GGAAGGACACCCGAAGAAAGG[SpacerC12]CCGAAACAGGGTTTTCACC |
| PSTVd-HEG-HR | GCTGTCGCTTCGGCTAC[SpacerC12]TTCAGTTGTTTCCACCG |
| Locus: Escherichia coli str. K12 substr. DH10B (CP000948.1) | |
| Hinge primer | Primer sequence (5′ – 3′) |
| LZ-HF | CCAGCGCCCGTTG[dSpacer]CTCGGCGTTTCATCTGTG |
| LZ-HR | CGGTGATGGTGCTGC[dSpacer]AGATAACTGCCGTCACTCC |
| LZL-389 | ATGAAAGCTGGCTACAGGAAGGCC |
| LZR-653 | GGTTTATGCAGCAACGAGACGTCA |
| LZF-2 | CTCGGCGTTTCATCTGTG |
| LZR-2 | AGATAACTGCCGTCACTCC |
| LZF-0 | TCGGTTACGGCCAGG |
| LZR-0 | AGGCGGTTTTCTCCGG |
The bold letters in the sequence denotes the location of the blocking modification (um: unmodified, ab: dSpacer and HEG: SpacerC12). For the detection of PSTVd two modifications and a control were used: dSpacer (abasic furane), c12-Spacer (hexaethyleneglycol) or no modification. For the detection of E.coli, only the dSpacer was used. All oligonucleotides were HPLC purified.