TABLE 1.
Thermodynamic parameters of RNA duplexes containing N7-guanosine and reference duplexesa
| Duplexes (5′-3′) | The average of the curve fits | TM−1 versus log CT plots | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| −ΔH° (kcal/mol) | −ΔS° (eu) |  (kcal/mol)
|
TMb (°C) | −ΔH° (kcal/mol) | −ΔS° (eu) |  (kcal/mol)
|
TMb (°C) |  d (kcal/mol)
|
ΔTMb,d (°C) | |
| 5′ UCAGGCAGU 3′ AGUCCGUCA |
80.0 ± 2.0 | 213.0 ± 5.9 | 13.93 ± 0.17 | 68.6 | 77.6 ± 0.7 | 206.0 ± 2.1 | 13.74 ± 0.06 | 68.7 | 0.00 | 0.00 |
| 5′ UCAG7GCAGU 3′ AGUC CGUCA |
67.9 ± 3.4c | 188.8 ± 10.3 | 9.33 ± 0.30 | 50.3 | 56.7 ± 4.3 | 153.7 ± 13.4 | 9.01 ± 0.13 | 51.2 | 4.73 | 17.5 |
| 5′ UCAGGCAGU 3′ AGUCUGUCA |
83.5 ± 3.4 | 230.6 ± 10.4 | 12.03 ± 0.17 | 58.9 | 74.2 ± 1.4 | 202.0 ± 4.4 | 11.53 ± 0.08 | 59.4 | 0.00 | 0.0 |
| 5′ UCAG7GCAGU 3′ AGUC UGUCA |
69.9 ± 2.6 | 198.5 ± 8.0 | 8.32 ± 0.11 | 45.2 | 69.7 ± 2.8 | 198.0 ± 8.8 | 8.32 ± 0.06 | 45.2 | 3.21 | 14.2 |
| 5′ UCAGGCAGU 3′ AGUCAGUCA |
68.7 ± 8.3 | 194.2 ± 26.5 | 8.49 ± 0.15 | 46.1 | 69.3 ± 3.7 | 196.3 ± 11.8 | 8.45 ± 0.08 | 45.9 | 0.00 | 0.0 |
| 5′ UCAG7GCAGU 3′ AGUC AGUCA |
73.0 ± 4.3 | 204.9 ± 13.2 | 9.49 ± 0.27 | 50.1 | 66.9 ± 4.7 | 185.6 ± 14.6 | 9.31 ± 0.17 | 50.4 | −0.86 | −4.5 |
| 5′ UCAGGCAGU 3′ AGUCGGUCA |
77.3 ± 1.9 | 217.4 ± 5.8 | 9.92 ± 0.11 | 51.2 | 85.0 ± 2.5 | 240.9 ± 7.7 | 10.30 ± 0.12 | 51.4 | 0.00 | 0.0 |
| 5′ UCAG7GCAGU 3′ AGUC GGUCA |
80.7 ± 9.1 | 222.6 ± 27.6 | 11.65 ± 0.51 | 58.0 | 73.9 ± 2.2 | 202.1 ± 6.6 | 11.25 ± 0.11 | 58.1 | −0.95 | −6.7 |
| 5′ UCACGGAGU 3′ AGUGCCUCA |
86.9 ± 2.9 | 234.1 ± 8.6 | 14.34 ± 0.35 | 67.6 | 76.8 ± 6.7 | 204.2 ± 19.8 | 13.46 ± 0.60 | 67.7 | 0.00 | 0.0 |
| 5′ UCAC7GGAGU 3′ AGUG CCUCA |
69.1 ± 7.4c | 192.6 ± 22.5 | 9.35 ± 0.43 | 50.2 | 57.1 ± 2.9 | 155.7 ± 8.8 | 8.84 ± 0.11 | 50.1 | 4.62 | 17.6 |
| 5′ UCACGGAGU 3′ AGUGUCUCA |
81.4 ± 6.3 | 226.4 ± 10.1 | 11.19 ± 0.40 | 55.8 | 78.2 ± 3.4 | 216.8 ± 10.5 | 11.01 ± 0.20 | 55.8 | 0.00 | 0.0 |
| 5′ UCAC7GGAGU 3′ AGUG UCUCA |
73.8 ± 4.3 | 208.0 ± 13.2 | 9.31 ± 0.20 | 49.1 | 71.3 ± 4.7 | 200.3 ± 14.8 | 9.24 ± 0.20 | 49.2 | 1.77 | 6.7 |
| 5′ UCACGGAGU 3′ AGUGACUCA |
62.5 ± 2.7 | 175.6 ± 8.5 | 8.01 ± 0.10 | 44.5 | 68.2 ± 7.7 | 193.9 ± 20.4 | 8.03 ± 0.20 | 44.0 | 0.00 | 0.0 |
| 5′ UCAC7GGAGU 3′ AGUGACUCA |
74.8 ± 8.4 | 209.6 ± 26.4 | 9.77 ± 0.30 | 51.0 | 65.4 ± 1.9 | 180.4 ± 5.9 | 9.44 ± 0.10 | 51.4 | −1.39 | −6.5 |
| 5′ UCACGGAGU 3′ AGUGGCUCA |
93.0 ± 11.6 | 268.2 ± 36.2 | 9.85 ± 0.41 | 48.5 | 84.8 ± 9.3 | 242.2 ± 29.3 | 9.72 ± 0.30 | 49.1 | 0.00 | 0.0 |
| 5′ UCAC7GGAGU 3′ AGUG GCUCA |
88.8 ± 11.7c | 247.1 ± 36.3 | 12.17 ± 0.46 | 58.0 | 74.4 ± 13.2 | 202.8 ± 40.1 | 11.48 ± 0.84 | 59.1 | −1.76 | −10.0 |
| 5′ UCAAGUAGU 3′ AGUUCAUCA |
83.3 ± 4.4 | 234.8 ± 13.7 | 10.51 ± 0.22 | 52.6 | 75.7 ± 10.3 | 211.3 ± 31.8 | 10.51 ± 0.46 | 52.6 | 0.00 | 0.00 |
| 5′ UCAA7GUAGU 3′ AGUU CAUCA |
53.6 ± 9.6 | 154.9 ± 31.6 | 5.50 ± 0.19 | 31.2 | 60.2 ± 6.1 | 176.7 ± 20.3 | 5.40 ± 0.19 | 31.3 | 5.11 | 21.3 |
| 5′ UCAAGUAGU 3′ AGUUUAUCA |
68.2 ± 4.1 | 197.1 ± 12.9 | 7.10 ± 0.10 | 39.6 | 72.7 ± 3.4 | 211.6 ± 10.9 | 7.08 ± 0.10 | 39.4 | 0.00 | 0.0 |
| 5′ UCAA7GUAGU 3′ AGUU UAUCA |
69.3 ± 16.8 | 204.4 ± 55.1 | 5.90 ± 0.30 | 34.2 | 64.1 ± 12.2 | 187.5 ± 39.7 | 5.93 ± 0.44 | 34.1 | 1.16 | 5.4 |
| 5′ UCAAGUAGU 3′ AGUUAAUCA |
43.9 ± 1.5 | 127.0 ± 4.5 | 4.50 ± 0.10 | 23.4 | 43.8 ± 6.6 | 126.6 ± 22.4 | 4.52 ± 0.50 | 23.4 | 0.00 | 0.0 |
| 5′ UCAA7GUAGU 3′ AGUU AAUCA |
52.2 ± 7.2 | 152.7 ± 23.5 | 4.80 ± 0.20 | 27.2 | 50.4 ± 7.5 | 146.8 ± 24.8 | 4.88 ± 0.40 | 27.2 | −0.36 | −3.8 |
| 5′ UCAAGUAGU 3′ AGUUGAUCA |
40.2 ± 7.4 | 108.7 ± 23.9 | 6.45 ± 0.16 | 36.4 | 46.0 ± 3.4 | 127.5 ± 11.2 | 6.43 ± 0.11 | 36.3 | 0.00 | 0.0 |
| 5′ UCAA7GUAGU 3′ AGUU GAUCA |
65.0 ± 4.7 | 184.3 ± 14.5 | 7.87 ± 0.28 | 43.5 | 57.3 ± 9.9 | 159.8 ± 31.5 | 7.77 ± 0.38 | 43.9 | −1.34 | −7.6 |
| 5′ UCAUGAAGU 3′ AGUACUUCA |
85.1 ± 3.7 | 240.3 ± 11.3 | 10.56 ± 0.22 | 52.4 | 76.2 ± 3.1 | 212.7 ± 9.5 | 10.24 ± 0.11 | 52.9 | 0.00 | 0.0 |
| 5′ UCAU7GAAGU 3′ AGUA CUUCA |
46.8 ± 6.2 | 135.2 ± 20.6 | 4.85 ± 0.24 | 26.2 | 46.0 ± 3.2 | 132.7 ± 10.9 | 4.86 ± 0.17 | 26.1 | 5.38 | 26.8 |
| 5′ UCAUGAAGU 3′ AGUAUUUCA |
52.8 ± 9.2 | 148.2 ± 30.2 | 6.48 ± 0.29 | 38.8 | 49.5 ± 7.9 | 137.2 ± 25.9 | 6.95 ± 0.44 | 39.6 | 0.00 | 0.0 |
| 5′ UCAU7GAAGU 3′ AGUA UUUCA |
57.1 ± 3.6c | 170.5 ± 12.5 | 4.23 ± 0.36 | 25.0 | 66.9 ± 19.4 | 204.0 ± 65.3 | 3.68 ± 0.30 | 24.3 | 3.27 | 13.8 |
| 5′ UCAUGAAGU 3′ AGUAAUUCA |
60.2 ± 8.4 | 170.1 ± 25.9 | 7.35 ± 0.24 | 41.3 | 58.4 ± 8.5 | 132.1 ± 28.7 | 7.48 ± 0.80 | 43.2 | 0.00 | 0.0 |
| 5′ UCAU7GAAGU 3′ AGUA AUUCA |
48.6 ± 2.0 | 143.9 ± 6.7 | 3.97 ± 0.13 | 21.5 | 53.0 ± 5.4 | 158.9 ± 18.5 | 3.72 ± 0.35 | 21.4 | 3.76 | 21.8 |
| 5′ UCAUGAAGU 3′ AGUAGUUCA |
62.1 ± 8.1 | 175.9 ± 26.1 | 7.58 ± 0.29 | 42.3 | 54.7 ± 4.6 | 152.5 ± 14.8 | 7.44 ± 0.13 | 42.2 | 0.00 | 0.0 |
| 5′ UCAU7GAAGU 3′ AGUA GUUCA |
49.3 ± 6.4 | 135.9 ± 20.9 | 7.17 ± 0.18 | 41.1 | 54.1 ± 2.5 | 151.3 ± 7.9 | 7.21 ± 0.04 | 40.9 | 0.23 | 1.3 |
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aSolutions 1 M sodium chloride, 20 mM sodium cacodylate, 0.5 mM Na2EDTA, pH 7.
-
bCalculated for 10−4 M oligomer concentration.
-
cDuplexes not performing two-state melting.
-
dThe free energies and the melting temperatures of 7G duplexes were compared to respective duplex containing guanosine.
