Table 3. INN Parameters for Canonical Base Pairs in 1 M NaCl without a Separate Parameter for Terminal GU Pairs.
| INN | INN counts | ΔG°37(kcal/mol) | ΔG°37 error (kcal/mol) | ΔH° (kcal/mol) | ΔH° error (kcal/mol) | ΔS°a(eu) | ΔS° error (eu) |
|---|---|---|---|---|---|---|---|
| Watson–Crick Nearest Neighbor Doublets | |||||||
| 5′AA3′ | –0.93 (−0.96) | 0.03 (0.03) | –6.82 (−7.09) | 0.79 (0.77) | –19.0 (−19.8) | 2.5 (2.4) | |
| 3′UU5′ | |||||||
| 5′AU3′ | –1.10 (−1.09) | 0.08 (0.07) | –9.38 (−9.11) | 1.68 (1.56) | –26.7 (−25.8) | 5.2 (4.8) | |
| 3′UA5′ | |||||||
| 5′UA3′ | –1.33 (−1.39) | 0.09 (0.08) | –7.69 (−8.50) | 2.02 (1.86) | –20.5 (−22.9) | 6.3 (5.7) | |
| 3′AU5′ | |||||||
| 5′CU3′ | –2.08 (−2.07) | 0.06 (0.06) | –10.48 (−10.90) | 1.24 (1.15) | –27.1 (−28.5) | 3.8 (3.5) | |
| 3′GA5′ | |||||||
| 5′CA3′ | –2.11 (−2.11) | 0.07 (0.06) | –10.44 (−11.03) | 1.28 (1.18) | –26.9 (−28.8) | 3.9 (3.6) | |
| 3′GU5′ | |||||||
| 5′GU3′ | –2.24 (−2.27) | 0.06 (0.05) | –11.40 (−11.98) | 1.23 (1.12) | –29.5 (−31.3) | 3.9 (3.5) | |
| 3′CA5′ | |||||||
| 5′GA3′ | –2.35 (−2.39) | 0.06 (0.05) | –12.44 (−13.21) | 1.20 (1.05) | –32.5 (−34.9) | 3.7 (3.2) | |
| 3′CU5′ | |||||||
| 5′CG3′ | –2.36 (−2.38) | 0.09 (0.09) | –10.64 (−10.88) | 1.65 (1.54) | –26.7 (−27.4) | 5.0 (4.7) | |
| 3′GC5′ | |||||||
| 5′GG3′ | –3.26 (−3.31) | 0.07 (0.06) | –13.39 (−14.18) | 1.24 (1.07) | –32.7 (−35.0) | 3.8 (3.3) | |
| 3′CC5′ | |||||||
| 5′GC3′ | –3.42 (−3.46) | 0.08 (0.07) | –14.88 (−16.04) | 1.58 (1.33) | –36.9 (−40.6) | 4.9 (4.0) | |
| 3′CG5′ | |||||||
| GU Nearest Neighbor Doublets | |||||||
| 5′GU3′ | 8 | 0.72 | 0.19 | –13.83 | 4.21 | –46.9 | 13.0 |
| 3′UG5′ | |||||||
| 5′GG3′ | 9 | –0.25 | 0.16 | –17.82 | 3.75 | –56.7 | 11.6 |
| 3′UU5′ | |||||||
| 5′AG3′ | 22 | –0.35 | 0.08 | –3.96 | 1.73 | –11.6 | 5.3 |
| 3′UU5′ | |||||||
| 5′UG3′ | 18 | –0.39 | 0.09 | –0.96 | 1.80 | –1.8 | 5.5 |
| 3′AU5′ | |||||||
| 5′UU3′ | 26 | –0.51 | 0.08 | –10.38 | 1.79 | –31.8 | 5.5 |
| 3′AG5′ | |||||||
| 5′UG3′ | 10 | –0.57 | 0.19 | –12.64 | 4.01 | –38.9 | 12.3 |
| 3′GU5′ | |||||||
| 5′AU3′ | 24 | –0.90 | 0.08 | –7.39 | 1.65 | –21.0 | 5.1 |
| 3′UG5′ | |||||||
| 5′CG3′ | 26 | –1.25 | 0.09 | –5.56 | 1.68 | –13.9 | 5.1 |
| 3′GU5′ | |||||||
| 5′CU3′ | 21 | –1.77 | 0.09 | –9.44 | 1.76 | –24.7 | 5.4 |
| 3′GG5′ | |||||||
| 5′GG3′ | 24 | –1.80 | 0.09 | –7.03 | 1.75 | –16.8 | 5.4 |
| 3′CU5′ | |||||||
| 5′GU3′ | 25 | –2.15 | 0.10 | –11.09 | 1.78 | –28.8 | 5.4 |
| 3′CG5′ | |||||||
| 5′GGUC3′b | 3 | –4.12 | 0.54 | –30.80 | 8.87 | –86.0 | 23.7 |
| 3′CUGG5′ | |||||||
| Other Nearest Neighbor Parameters | ||||||
|---|---|---|---|---|---|---|
| initiationc | 4.09 (4.23) | 0.22 (0.20) | 3.61 (6.40) | 4.12 (3.56) | –1.5 (6.99) | 12.7 (10.9) |
| terminal AU penaltyc | 0.45 (0.43) | 0.04 (0.04) | 3.72 (3.85) | 0.83 (0.77) | 10.5 (11.04) | 2.6 (2.4) |
| symmetryc | 0.43 | 0 | 0 | 0 | –1.4 | 0 |
a
Values for ΔS° were derived from ΔS° = (ΔH° – ΔG°37)/310.15.
b
Ref (12).
c
Values for initiation, terminal AU, and nearest neighbors with only Watson–Crick pairs are from ref (11) when not in parentheses and derived from an expanded database when in parentheses. Values for nearest neighbors with GU pairs were derived using the Xia et al. parameters11 for Watson–Crick nearest neighbors.