Table 2. Thermodynamic parameters for helix formation with R6A-U at terminal base pair position and R6A as 3′-dangling endsa,b.
| R = | Terminal R6A-U: (UACAUGUR6A)2 | 3′-dangling end R6A: (ACAUGUR6A)2 | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| –ΔH0 (kcal/mol) | –ΔS0 (eu) | –ΔG037 (kcal/mol) | TMc (°C) | ΔΔG037 (kcal/mol) | –ΔH0 (kcal/mol) | –ΔS0 (eu) | –ΔG037 (kcal/mol) | TMc (°C) | ΔΔG037 (kcal/mol) | |
| Methyl- | 57.5 ± 1.4 | 165.4 ± 4.6 | 6.20 ± 0.01 | 39.9 | 0.76 | 62.0 ± 1.8 | 181.3 ± 5.9 | 5.79 ± 0.02 | 37.6 | –0.09 |
| Neopentyl- | 62.0 ± 2.5 | 180.8 ± 8.2 | 5.94±0.04 | 38.3 | 1.02 | 60.4 ± 2.0 | 177.0 ± 6.7 | 5.50 ± 0.04 | 36.1 | 0.20 |
| 1-Methylpropyl- | 59.3 ± 2.5 | 173.6 ± 8.2 | 5.46 ± 0.05 | 35.9 | 1.50 | 61.3 ± 1.8 | 181.5 ± 5.9 | 4.96 ± 0.04 | 33.4 | 0.74 |
| 1-Methylbutyl- | 59.5 ± 2.0 | 174.7 ± 6.4 | 5.33 ± 0.04 | 35.2 | 1.63 | 63.3 ± 1.8 | 188.7 ± 6.0 | 4.76 ± 0.05 | 32.6 | 0.94 |
| Isopentyl- | 60.9 ± 1.8 | 176.8 ± 5.9 | 6.10 ± 0.02 | 39.2 | 0.86 | 59.0 ± 1.7 | 172.2 ± 5.5 | 5.60 ± 0.03 | 36.6 | 0.10 |
| Isopentenyl- | 53.0 ± 3.0 | 151.3 ± 9.9 | 6.02 ± 0.06 | 39.0 | 0.94 | 52.2 ± 3.1 | 149.6 ± 9.9 | 5.85 ± 0.06 | 38.1 | –0.15 |
| Propargyl- | 62.4 ± 1.6 | 181.8 ± 5.3 | 5.98 ± 0.02 | 38.5 | 0.98 | 65.5 ± 1.9 | 193.3 ± 6.2 | 5.52 ± 0.03 | 36.3 | 0.18 |
| (UACAUGUA)2 | 56.2 ± 1.6 | 158.7 ± 5.2 | 6.96 ± 0.02 | 44.3 | 0 | |||||
| (ACAUGUA)2 | 50.9 ± 1.0 | 145.8 ± 3.1 | 5.70 ± 0.01 | 37.1 | 0 | |||||
aSolutions are 1 M sodium chloride, 20 mM sodium cacodylate and 0.5 mM Na2EDTA, pH 7.
bThermodynamic parameters were calculated from TM–1 versus log CT plots.
cMelting temperatures were calculated for 10–14 M oligomer concentration.