Table 1. List of oligonucleotides used in this study.
| Oligonucleotide | No. of plasmid-binding sites | Description | Sequence |
|---|---|---|---|
| LNA2 | 8 | 9mer 100% LNA | 5′-TAMRA-CTCTCTCTC-3′ |
| LNA4 | 6 | 13mer 100% LNA | 5′-TAMRA-CTCTCTCTCTCTC-3′ |
| LNA5 | 4 | 17mer 50% LNA | 5′-TAMRA-CtCtCtCtCtCtCtCtC-3′ |
| LNA6 | 6 | 13mer 100% LNA | 5′-NH2-CTCTCTCTCTCTC-3′ |
| LNA7 | 5 | 14mer 100% LNA | 5′-NH2-CCTTCCTTCCTTCC-3′ |
| LNA8 | 6 | 13mer 100% LNA | 5′-NH2-GAGAGAGAGAGAG-3′ |
| LNA9 | 6 | 11mer 100% LNA | 5′-NH2-CTCTCTCTCTC-3′ |
| LNA9R | 6 | 11mer 100% LNA | 5′-TAMRA-CTCTCTCTCTC-3′ |
| LNA10 | 8 | 9mer ‘bis’ 50% LNA, 50% DNA | 5′-NH2-CtCtCtCtC-XXX- CtCtCtCtC-3′ |
| LNA11 | 5 | 14mer 100% LNA | 5′-NH2-GGAAGGAAGGAAGG-3′ |
| PTOCpG–LNA | 6 | 20mer PTO, 1mer DNA, 13mer LNA | 5′-tccatgacgttcctgacgtttGAGAGAGAGAGAG-3′ |
| PTOGpC–LNA | 6 | 20mer PTO, 1mer DNA, 13mer LNA | 5′-tccatgagcttcctgagtcttGAGAGAGAGAGAG-3′ |
| CpG1826 | – | 20mer 100% PTO | 5′-tccatgacgttcctgacgtt-3′ |
| GpC1745 | – | 20mer 100% PTO | 5′-tccatgagcttcctgagtct-3′ |
| GTS PNA | 9–10 | 8mer ‘bis’ 100% PNA | 5′Rho-O-O-TCTCTCTC-O-O-O-JTJTJTJT-CONH2 |
| OsPNA2 | 6 | 13mer ‘bis’ 100% PNA | 5′ROX-O-O-gCTCTCTCTCTCTC-O-CTCTCTCTCTCTCk |
| OsPNA3 | 6 | 13mer 100% PNA | 5′ROX-O-O-gCTCTCTCTCTCTCk |
| OsPNA4 | 6 | 13mer ‘bis’ 100% PNA | 5′ROX-O-O-gCTCTCTCTCTCTC-O-O-O-CTCTCTCTCTCTCk |
| RevGG2B | 1 | 22mer 100% DNA | 5′(Cy5)-ggaaggaagttaggaaggaagg-3′ |
| KH2 | 4 | 19mer 100% DNA | 5′-Fl-gagagagagagagagagag- 3′ |
| KH3 | 3 | 18mer 100% DNA | 5′-Fl-ggaaggaaggaaggaagg- 3′ |
LNA residues are bold upper case; DNA residues are bold lower case; PTO residues are additionally italicised; PNA and amino acid residues are italicised, normal text, with PNA bases upper case. Numbers of binding sites refer to the maximum theoretical ODN-binding sites present on the GeneGrip plasmid series. O = 8-amino-3, 6-dioxaoctanoic acid linker; J = pseudoisocytosine; g = glycine; k = lysine; X = ‘PEG spacer’ -9-O-dimethoxytrityl-triethyleneglycol, 1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite, spacer phosphoramidate 9; Fl = fluorescein, Rho = rhodamine, TAMRA = carboxytetramethylrhodamine, ROX = carboxy-X-rhodamine, NH2 = 5′-amino-modifier C12 phosphoramidite spacer.