Table 1.
LNAs and the corresponding sequences used in this work
Group 1 ONs | Target sequence: 5′-AAGAAGAAAA-3′ |
bisLNA-20 | Cy3-tTcTtCtTtT-ctctc-tTtTcTtCtT |
bisLNA-20a | Cy3-tTcTtCtTtT-ctctc-ttttcttctt |
bisLNA-20b | Cy3-ttcttctttt-ctctc-tTtTcTtCtT |
bisLNA-20c | Cy3-tTcTtCtTtT-s18-tTtTcTtCtT |
bisLNA-20d | Cy3-tTcTtCtTtT-s18-tTtTcTtCtT (fully phosphorothioated) |
bisLNA-20e | Cy3-tTcTtCtTtT-s18±s9-tTtTcTtCtT |
TFO-LNA-20 | Cy3-tTcTtCtTtT |
WC-LNA-20 | Cy5-tTtTcTtCtT |
Group 2 ONs | Target sequence: 5′-GCAGAGGGCGTGGGGGAAAAGAAAAAAGA-3′ |
bisLNA-m30 | Cy3-cCtTtTcTtTtTtCt-tctct-TcTtTtTtCtTtTcC |
bisLNA-m44 | Cy3-CcTtTtCtTtTtTcT-tctct-tCtTtTtTcTtTtCcCccAcgCccTctGc |
bisLNA-m44a | Cy3-CcTtTtCtTtTtTcT-tctct-TcTtTtTtCtTtTcCCccAcgCccTctGc |
bisLNA-m44b | Cy3-cCtTtTcTtTtTtCt-tctct-TcTtTtTtCtTtTcCCccAcgCccTctGc |
bisLNA-m44c | Cy3-CcTtTtCtTtTtTcT-tctct-TcTtTtTtCtTtTccCccAcgCccTctGc |
bisLNA-m44d | Cy3-cCtTtTcTtTtTtCt-tctct-tCtTtTtTcTtTtCcCccAcgCccTctGc |
bisLNA-m44e | Cy3-CcTtTtCtTtTtTcT-tctct-tCtTtTtTcTtTtCcCccACgCCcTCtGC |
bisLNA-m44-3t | Cy3-tTtCtTtTtTcT-tctct-tCtTtTtTcTtTtCcCccAcgCccTctGc |
bisLNA-m44-7w | Cy3-CcTtTtCtTtTtTcT-tctct-tCtTtTtTcTtTtCcCccAcgC |
WC-LNA-m30 | Cy5-TcTtTtTtCtTtTcC |
WC-LNA-m44 | Cy5-tCtTtTtTcTtTtCcCccAcgCccTctGc |
TFO-LNA-m30/44 | Cy3-cCtTtTcTtTtTtCt |
Group 3 ONs | Target sequence: 5′-GGGAAAAAGAACGGAGGGAGGGA-3′ |
bisLNA-m(P2)37 | Cy3-CcTcCcTcCcT-tctctc-TcCcTcCcTcCgTtCtTtTtCcCgCc |
LNA bases are in capital letters; DNA bases in small letters; linker sequence/region is underlined; s18 = hexaethylene glycyl linker; s18 + s9 = hexaethylene glycyl extended with a triethylene glycyl linker; target sequence of group 2 and 3 LNAs shown in italic corresponds to the complementary region of the extended Watson–Crick arm of bisLNA-m44.
Rational behind designations: m indicates a bisLNA targeting a MYC sequence, numbers correspond to number of nucleotides without those in the linker, t and w indicate the nature of the altered arm (TFO or WC, respectively) followed by the reduced number of nucleotides in the arm.