Table 2.
Thermodynamic parameters of heteroduplexes of RNA and 2′-O-methyl oligoribonucleotides a
| Duplexes | Average of curve fits
|
TM−1 vs log CT plots
|
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|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RNA | 2′OMeRNA | −ΔH° (kcal/mol) |
−ΔS° (eu) | −ΔG°37 (kcal/mol) |
TMb (°C) |
−ΔH° (kcal/mol) |
−ΔS° (eu) | −ΔG°37 (kcal/mol) |
TMb (°C) |
ΔΔG°c37 (kcal/mol) |
ΔTMb,c (°C) |
|
| Probe 40 | mimics | |||||||||||
| A-U | 5′CCAUGCC | 5′GGCAUGG | 69.1±2.5 | 190.9±7.7 | 9.86±0.13 | 52.7 | 64.1±3.1 | 175.6±9.6 | 9.69±0.11 | 53.1 | ||
| A-s2U | 5′CCAUGCC | 5′GGCAs2UGG | 75.1±13.5 | 206.2±40.6 | 11.16±0.90 | 57.4 | 83.1±13.8 | 230.6±41.8 | 11.56±0.87 | 57.0 | −1.87 | 3.9 |
|
| ||||||||||||
| G-U | 5′CCGUGCC | 5′GGCAUGG | 61.5±2.2 | 173.1±7.1 | 7.78±0.05 | 43.4 | 58.4±1.6 | 163.2±4.9 | 7.76±0.01 | 43.7 | ||
| G-s2U | 5′CCGUGCC | 5′GGCAs2UGG | 61.1±3.7 | 171.9±11.9 | 7.80±0.07 | 43.6 | 56.9±4.02 | 158.6±12.7 | 7.73±0.09 | 43.7 | +0.03 | 0 |
|
| ||||||||||||
| C→U in | probe 40 | |||||||||||
| A-U | 5′CCAUACC | 5′GGUAUGG | 64.7±2.1 | 181.4±6.8 | 8.41±0.06 | 46.3 | 57.2±2.7 | 157.4±8.7 | 8.34±0.04 | 47.2 | ||
| A-s2U | 5′CCAUACC | 5′GGs2UAUGG | 65.1±3.3 | 179.9±10.3± | 9.27±0.19 | 50.6 | 58.8±0.9 | 160.5±2.9 | 9.05±0.03 | 50.9 | −0.71 | 3.7 |
|
| ||||||||||||
| G-U | 5′CCAUGCC | 5′GGUAUGG | 77.9±17.3 | 231.2±56.1 | 6.19±0.10 | 35.7 | 69.6±4.2 | 204.5±13.9 | 6.22±0.08 | 35.6 | ||
| G-s2U | 5′CCAUGCC | 5′GGs2UAUGG | 76.9±14.7 | 229.1±47.7 | 5.80±0.07 | 34.1 | 77.9±8.6 | 232.6±27.9 | 5.82±0.13 | 34.2 | +0.4 | −1.7 |
|
| ||||||||||||
| Probe 56 | mimics | |||||||||||
| A-U | 5′AGUGAAA | 5′UUUCACU | 59.7±6.7 | 177.7±22.6 | 4.60±0.35 | 27.3 | 56.4±3.5 | 166.3±11.9 | 4.79±0.16 | 27.7 | ||
| A-s2U | 5′AGUGAAA | 5′Us2UUCACs2U | 53.9±8.0 | 154.4±25.8 | 6.07±0.13 | 34.4 | 48.5±6.5 | 136.7±21.4 | 6.11±0.30 | 34.3 | −1.32 | 6.6 |
| A-s2U | 5′AGUGAAA | 5′s2UUs2UCACs2U | 59.4±3.8 | 169.8±12.2 | 6.70±0.06 | 37.9 | 54.5±1.7 | 153.7±5.6 | 6.77±0.03 | 38.4 | −1.98 | 10.7 |
| A-s2U | 5′AGUGAAA | 5′s2Us2Us2UCACs2U | 64.5±4.8 | 181.8±15.4 | 8.10±0.09 | 44.8 | 60.2±1.6 | 168.1±5.1 | 8.04±0.02 | 45.0 | −3.25 | 17.3 |
a
Solutions are 100 mM NaCl, 20 mM sodium cacodylate, and 0.5 mM Na2EDTA, pH 7.
b
Calculated for 10−4 M oligonucleotide concentration.
c
Differences due to substitution of U with s2U.