Table 1.
Thermal stability (Tm) and inhibition efficiency of ONs synthesizeda
| Sequence | ON6 | ON7 | ON8 | ON9 | ON10 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3′-cPaccPu | 3′-cPacPaccPuu | 3′-CPACPACCPTT | 3′-cacaccuu | 3′-CACACCTT | ||||||||
| 0%b | 80% | 56% | 0% | |||||||||
| ON1 | 5′-gPuggPA3d | 18.0c | 29.5 | <5.0 | 21.0 | 13.5 | ||||||
| 42% | 72% | 46% | ||||||||||
| ON2 | 5′-gPugPuggPaA3d | 26.0 | 42.0 | 21.5 | 35.1 | 31.5 | ||||||
| 90% | 94% | 96% | 96% | 92% | ||||||||
| ON3 | 5′-GPTGPTGGPAA | <5.0 | <5.0 | 21.0 | <5.0 | 41.5 | ||||||
| 67% | 72% | 88% | 84% | 77% | ||||||||
| ON4 | 5′-guguggaA3d | 25.5 | 37.5 | 24.0 | 55.5 | 36.5 | ||||||
| 19% | 25% | 83% | 62% | 25% | ||||||||
| ON5 | 5′-GTGTGGAA | <5.0 | 19.5 | 39.0 | 21.0 | 26.0 | ||||||
aP denotes INA monomer; A3d denotes 3′-deoxyadenosine; g, u, a, c denote 2′-O-methylribonucleotides; G, T, A, C denote 2′-deoxyribonucleotides. ON1-5 are complements to the template strand; ON6-10 are complements to the non-template strand.
bInhibition efficiencies are showed in the right lower corner of the cell in italic and defined as percentage decrease of transcription relative to noninhibited RNA transcription at 10 µM concentration of inhibitor.
cTms (°C), which are showed in the left upper corner of the cell, were determined at 260 nm as the maximum of the first derivative plots of the melting curves obtained by measuring absorbance at 260 nm against increasing temperature (1.0°C min−1) on equimolar mixtures (1.0 µM in each strand) of ON1-10 in a hybridization buffer (40 mM Tris–HCl, 100 mM KCl, 10 mM MgCl2, pH 7.9). The bold Tm values represent easily denaturing nucleic acids. The underlined values of Tm represent the expanded list of easily denaturing nucleic acids (see text for details).