Table 4.
Measured and predicted thermodynamic parameters for test sequence duplex formationa
| Average of curve fits |
Tm−1
vs log Ct plots |
|||||||
|---|---|---|---|---|---|---|---|---|
| Sequences | −ΔHo (kcal/mol) | −ΔSo (e.u.) | −ΔGo (kcal/mol) | Tmb (°C) | −ΔHo (kcal/mol) | −ΔSo (e.u.) | −ΔGo37 (kcal/mol) | Tmb (°C) |
| UGAGUAC | 50.8 | 145.0 | 5.8 | 32.6 | 44.1 | 122.6 | 6.1 | 33.7 |
| UUGCUCG | (35.2) | (98.0) | (4.8) | (22.6) | ||||
| (37.6) | (104.2) | (5.2) | (27.2) | |||||
| UGAGUAA | 54.5 | 156.9 | 5.8 | 33.0 | 41.6 | 115.3 | 5.9 | 32.3 |
| GUGCUCG | (35.2) | (98.0) | (4.8) | (22.6) | ||||
| (38.6) | (106.7) | (5.4) | (29.1) | |||||
| UGAGUUC | 55.7 | 162.3 | 5.4 | 30.5 | 57.2 | 167.0 | 5.4 | 30.9 |
| AGGCUCG | (34.9) | (98.2) | (4.5) | (19.6) | ||||
| (37.3) | (104.7) | (4.9) | (23.6) | |||||
| UACAGGC | 54.7 | 159.9 | 5.1 | 29.0 | 48.8 | 140.6 | 5.2 | 28.8 |
| AAGUGUC | (41.0) | (117.2) | (4.7) | (23.5) | ||||
| (43.5) | (123.9) | (5.2) | (27.0) | |||||
| UGCUGAU | 49.9 | 142.6 | 5.6 | 31.6 | 53.8 | 155.1 | 5.7 | 32.1 |
| UGACGAU | (39.8) | (112.5) | (4.9) | (25.6) | ||||
| (42.3) | (119.2) | (5.4) | (28.6) | |||||
aSolutions are 1.0 M NaCl, 10 mM sodium cacodylate, 0.5 mM EDTA pH 7.
bCalculated at 10−4 M oligomer concentration. Values in parenthesis are predicted: top row is the predicted values for single 3′ terminal overhang duplexes and bottom row is the predicted values as described in the text for duplexes with 3′ double overhangs.