Table 1.
Thermodynamic parameters for duplex formation in 1 M NaCla
| Average of curve fits |
Tm−1 versus log Ct plots |
|||||||
|---|---|---|---|---|---|---|---|---|
| Sequences | −ΔHo (kcal/mol) | −ΔSo (e.u.) | −ΔGo37 (kcal/mol) | Tmb (°C) | −ΔHo (kcal/mol) | −ΔSo (e.u.) | −ΔGo37 (kcal/mol) | Tmb (°C) |
| (UGGCCGAA)2 | 53.2 ± 1.1 | 140.5 ± 3.2 | 9.6 ± 0.1 | 61.9 | 55.1 ± 3.3 | 146.2 ± 9.9 | 9.7 ± 0.2 | 61.7 |
| (UGGCCGAG)2 | 52.9 ± 2.1 | 139.8 ± 6.0 | 9.6 ± 0.2 | 61.7 | 64.8 ± 3.1 | 175.8 ± 9.3 | 10.2 ± 0.2 | 60.5 |
| (UGGCCGAC)2 | 52.1 ± 0.8 | 137.8 ± 2.2 | 9.3 ± 0.2 | 60.4 | 60.5 ± 3.4 | 163.1 ± 10.2 | 9.9 ± 0.2 | 60.1 |
| (UGGCCGAU)2 | 54.1 ± 1.0 | 143.1 ± 2.8 | 9.7 ± 0.2 | 62.1 | 64.0 ± 2.5 | 173.1 ± 7.6 | 10.3 ± 0.2 | 61.2 |
| (UGGCCGA)2 | 52.4 ± 1.1 | 139.5 ± 3.4 | 9.2 ± 0.1 | 59.1 | 60.8 ± 1.1 | 164.9 ± 3.3 | 9.7 ± 0.1 | 58.9 |
| (UGGCCGGA)2 | 57.4 ± 3.5 | 153.2 ± 10.7 | 9.9 ± 0.3 | 61.4 | 62.0 ± 4.0 | 167.4 ± 12.1 | 10.1 ± 0.2 | 61.0 |
| (UGGCCGGG)2 | 51.9 ± 1.4 | 137.3 ± 4.4 | 9.3 ± 0.1 | 60.5 | 53.2 ± 1.4 | 141.4 ± 4.1 | 9.4 ± 0.1 | 60.2 |
| (UGGCCGGC)2 | 55.5 ± 5.7 | 143.6 ± 5.7 | 11.0 ± 0.2 | 69.8 | 56.0 ± 3.3 | 145.2 ± 9.7 | 11.0 ± 0.3 | 69.5 |
| (UGGCCGGU)2 | 47.9 ± 4.1 | 124.7 ± 12.3 | 9.2 ± 0.3 | 62.0 | 52.0 ± 5.7 | 137.3 ± 17.4 | 9.5 ± 0.4 | 61.4 |
| (UGGCCGG)2 | 52.2 ± 3.1 | 139.2 ± 9.7 | 9.0 ± 0.2 | 58.3 | 57.5 ± 4.6 | 155.4 ± 14.0 | 9.3 ± 0.3 | 58.0 |
| (UGGCCGCA)2 | 54.2 ± 1.2 | 142.9 ± 3.8 | 9.9 ± 0.1 | 63.2 | 62.5 ± 0.7 | 167.8 ± 2.0 | 10.5 ± 0.0 | 62.9 |
| (UGGCCGCG)2 | 56.1 ± 2.0 | 149.2 ± 6.3 | 9.8 ± 0.0 | 61.9 | 65.6 ± 1.6 | 177.8 ± 4.8 | 10.5 ± 0.1 | 61.3 |
| (UGGCCGCC)2 | 54.4 ± 1.1 | 143.2 ± 3.5 | 10.0 ± 0.1 | 63.9 | 61.4 ± 2.0 | 164.4 ± 6.2 | 10.5 ± 0.1 | 63.2 |
| (UGGCCGCU)2 | 54.9 ± 1.7 | 145.6 ± 5.3 | 9.8 ± 0.1 | 61.8 | 55.9 ± 2.6 | 148.6 ± 7.8 | 9.8 ± 0.1 | 61.6 |
| (UGGCCGC)2 | 55.4 ± 0.9 | 147.1 ± 2.9 | 9.8 ± 0.1 | 62.0 | 63.2 ± 1.9 | 170.5 ± 5.6 | 10.3 ± 0.1 | 61.5 |
| (UGGCCGUA)2 | 52.3 ± 2.3 | 138.0 ± 7.2 | 9.5 ± 0.2 | 61.6 | 57.8 ± 1.9 | 154.7 ± 5.8 | 9.8 ± 0.1 | 61.1 |
| (UGGCCGUG)2 | 53.0 ± 3.8 | 140.4 ± 11.7 | 9.4 ± 0.2 | 60.6 | 54.5 ± 1.9 | 145.2 ± 5.9 | 9.4 ± 0.1 | 60.0 |
| (UGGCCGUC)2 | 53.1 ± 1.5 | 140.5 ± 4.8 | 9.6 ± 0.1 | 61.4 | 57.9 ± 1.5 | 155.1 ± 4.5 | 9.8 ± 0.1 | 60.9 |
| (UGGCCGUU)2 | 52.8 ± 2.1 | 139.5 ± 6.2 | 9.5 ± 0.2 | 61.3 | 57.0 ± 2.6 | 152.2 ± 8.0 | 9.7 ± 0.2 | 60.9 |
| (UGGCCGU)2 | 51.6 ± 2.5 | 136.9 ± 7.4 | 9.1 ± 0.3 | 59.1 | 59.8 ± 3.5 | 162.0 ± 10.8 | 9.6 ± 0.2 | 58.8 |
| (GGCGCUAA)2 | 67.6 ± 2.9 | 181.0 ± 8.8 | 11.4±.27 | 65.7 | 69.7 ± 5.5 | 187.4 ± 16.5 | 11.5 ± 0.4 | 65.4 |
| (GGCGCUAG)2 | 63.8 ± 8.7 | 172.0 ± 26.8 | 10.5 ± 0.4 | 62.1 | 67.8 ± 10.6 | 183.8 ± 31.6 | 10.8 ± 0.8 | 62.2 |
| (GGCGCUAC)2 | 68.2 ± 2.6 | 183.4 ± 7.9 | 11.3 ± 0.4 | 64.7 | 65.3 ± 6.6 | 174.7 ± 20.1 | 11.1 ± 0.5 | 65.1 |
| (GGCGCUAU)2 | 60.6 ± 6.1 | 161.1 ± 18.4 | 10.6 ± 0.4 | 64.7 | 61.7 ± 3.6 | 164.5 ± 10.9 | 10.7 ± 0.2 | 64.3 |
| (GGCGCUA)2 | 60.9 ± 2.8 | 163.8 ± 8.6 | 10.2 ± 0.2 | 61.7 | 62.9 ± 3.8 | 169.8 ± 11.4 | 10.3 ± 0.2 | 61.4 |
| (GGCGCUGA)2 | 65.4 ± 2.1 | 177.1 ± 6.4 | 10.5 ± 0.2 | 61.5 | 74.4 ± 3.5 | 204.3 ± 10.7 | 11.1 ± 0.2 | 61.3 |
| (GGCGCUGG)2 | 61.9 ± 6.1 | 165.3 ± 18.2 | 10.6 ± 0.5 | 64.0 | 60.9 ± 5.3 | 162.6 ± 16.0 | 10.5 ± 0.4 | 63.7 |
| (GGCGCUGC)2 | 66.7 ± 2.9 | 179.7 ± 8.9 | 11.0 ± 0.2 | 63.7 | 75.8 ± 2.9 | 206.9 ± 8.8 | 11.6 ± 0.2 | 63.3 |
| (GGCGCUGU)2 | 60.3 ± 7.1 | 159.7 ± 21.5 | 10.8 ± 0.6 | 65.7 | 60.2 ± 4.9 | 159.4 ± 14.7 | 10.8 ± 0.3 | 65.7 |
| (GGCGCUG)2 | 65.4 ± 1.7 | 177.9 ± 5.6 | 10.3 ± 0.2 | 60.3 | 72.6 ± 10.3 | 199.8 ± 31.4 | 10.6 ± 0.5 | 59.8 |
| (GGCGCUCA)2 | 61.3 ± 6.5 | 165.9 ± 20.0 | 9.8 ± 0.3 | 59.4 | 65.6 ± 4.4 | 179.2 ± 13.6 | 10.1 ± 0.2 | 59.1 |
| (GGCGCUCG)2 | 57.8 ± 6.8 | 154.9 ± 20.0 | 9.7 ± 0.6 | 60.2 | 61.9 ± 4.8 | 167.4 ± 14.6 | 10.0 ± 0.3 | 60.4 |
| (GGCGCUCC)2 | 62.9 ± 6.4 | 170.2 ± 19.8 | 10.1 ± 0.4 | 60.4 | 59.6 ± 4.2 | 159.9 ± 12.8 | 9.9 ± 0.2 | 61.1 |
| (GGCGCUCU)2 | 57.8 ± 2.3 | 155.6 ± 6.7 | 9.5 ± 0.3 | 59.0 | 61.7 ± 5.4 | 167.6 ± 16.3 | 9.8 ± 0.3 | 58.9 |
| (GGCGCUC)2 | 63.4 ± 5.6 | 172.3 ± 16.7 | 9.9 ± 0.5 | 59.3 | 60.0 ± 6.0 | 162.2 ± 18.4 | 9.7 ± 0.3 | 59.4 |
| (GGCGCUUA)2 | 56.4 ± 9.6 | 150.0 ± 29.7 | 9.9 ± 0.5 | 62.0 | 55.7 ± 2.6 | 148.2 ± 7.9 | 9.7 ± 0.2 | 61.3 |
| (GGCGCUUG)2 | 59.0 ± 2.4 | 159.7 ± 7.6 | 9.5 ± 0.1 | 58.4 | 60.0 ± 4.1 | 164.7 ± 12.5 | 9.6 ± 0.2 | 58.2 |
| (GGCGCUUC)2 | 57.7 ± 3.8 | 155.4 ± 11.7 | 9.5 ± 0.2 | 58.0 | 63.4 ± 3.6 | 172.7 ± 10.9 | 9.8 ± 0.2 | 58.5 |
| (GGCGCUUU)2 | 54.8 ± 5.7 | 147.6 ± 17.7 | 9.0 ± 0.3 | 56.9 | 65.5 ± 5.2 | 180.5 ± 16.1 | 9.5 ± 0.3 | 56.2 |
| (GGCGCUU)2 | 57.3 ± 4.1 | 154.4 ± 12.5 | 9.4 ± 0.3 | 58.7 | 61.0 ± 5.1 | 165.7 ± 15.3 | 9.6 ± 0.3 | 58.6 |
aSolutions are 1.0 M NaCl, 10 mM sodium cacodylate, 0.5 mM EDTA pH 7.
bCalculated at 10−4 M oligomer concentration.
Thermodynamic values for (UGGCCG)2 are −51.4 kcal/mol, −138.5 e.u. and −8.4 kcal/mol for, ΔHo, ΔSo, and ΔGo37, respectively and for (GGCGCU)2 are −56.2 kcal/mol, −153.8, e. u. and −8.5 kcal/mol for ΔHo, ΔSo and ΔGo37, respectively (34).
Values in bold are 3′ overhangs, values in italics are non-two-state.