Table 1.
Oligonucleotide sequences
| Primers | Sequences (5′–3′) |
|---|---|
| ACTB* | C+GG+GC+GG+CG+GATCGGCAAAG |
| FANCD2_LNA | A+TG+GG+AA+TT+AT+GTAGTAACAATG |
| KAT6A_LNA | T+TT+CT+GC+AG+TG+CTTGTTCTT |
| Padlock probes | Sequences (5′–3′) |
|---|---|
| plp_ACTB* | AGCCTCGCCTTTGCCTTCCTTTTACGACCTCAATGCACATGTTTGGCTCCTCTTCGCCCCGCGAGCACAG |
| plp_FANCD2_WT | AAAAGACATCATTGTTCCTAGTAATCAGTAGCCGTGACTATCGACTGGTTCAAAGTCACAGGGAAGGAAG |
| plp_FANCD2_MUT | AAAAGACATCATTGTTTCCTTTTACGACCTCAATGCTGCTGCTGTACTACTCTTCTCACAGGGAAGGAAC |
| plp_KAT6A_WT | ATCATGACTGAGAAAGAAAAGTAGCCGTGACTATCGACTAATGCGTCTATTTAGTGGAGCCCACTATCTTTGGGAGCCAGGAA |
| plp_KAT6A_MUT | ATCATGACTGAGAAAGAAACCTCAATGCTGCTGCTGTACTACAATGCGTCTATTTAGTGGAGCCTTCTATCTTTGGGAGCCAGGAC |
| Detection probes | Sequences (5′–3′) |
|---|---|
| D1_ATTO 488 | Atto 488-CCTCAATGCACATGTTTGGCTCC |
| D2_ATTO 647N | Atto 647N-AGTAGCCGTGACTATCGACT |
| D3_ATTO 550 | Atto 550-CCTCAATGCTGCTGCTGTACTAC |
| D4_Cy3 | Cy3-AGTAGCCGTGACTATCGACT |
| D5_FITC | FITC-CCTCAATGCTGCTGCTGTACTAC |
Padlock probes were 5′-phosphorylated. The fluorophores of the detection oligos were 5′ conjugated
+: the following base is LNA modified; underlined: target complement sequence, bold: detection probe complement sequence
*Modified from (Grundberg et al. 2013)