Table 1. Thermodynamic parameters for formation of DNA–DNA and DNA–RNA duplexes from the single strands (DNA 1 + DNA 2/RNA 2) in 10 mM phosphate buffer pH 7.0, 100 mM NaCl (5 µM duplexes)a.
| Tm (°C)b | ΔH° (kJ/mol)b | TΔS° (kJ/mol)b | ΔG° (kJ/mol)b | ΔA260 (%)c | |||||
| DNA 1 sample |
DNA 2 |
RNA 2 |
DNA 2 |
RNA 2 |
DNA 2 |
RNA 2 |
DNA 2 |
RNA 2 |
DNA 2 |
| O-Propyl | 54.2 | 62.5 | –173.1 | –350.1 | –125.8 | –279.0 | –47.3 | –71.1 | 18.1 |
| O-Methoxyethyl | 57.9 | 72.4 | –187.0 | –312.9 | –136.4 | –238.0 | –50.6 | –74.9 | 19.4 |
| O-Aminopropyl | 39.7 | 41.1 | –223.5 | –208.4 | –180.9 | –165.8 | –42.6 | –42.6 | 12.6 |
| Control (P=O) | 36.3 | 31.6 | –260.0 | –207.9 | –218.6 | –171.4 | –41.4 | –36.5 | 15.3 |
| Fluoro (P=S) | 50.0 | n.d. | –152.5 | n.d. | –108.3 | n.d. | –44.2 | n.d. | 12.4 |
| Control (P=S) | 36.8 | 25.3 | –201.0 | –148.9 | –161.4 | –116.8 | –39.6 | –32.1 | 11.4 |
aDerived from Van’t Hoff plots for the formation of the duplexes using CD data.
bThe values given in parenthesis are the maximum uncertainties: Tm (± 1.5°C), ΔH° (± 10%), TΔS°(298 K) (± 10%) and ΔG°(298 K) (± 5%).
cThis column lists the observed absorbance hypochromicity [calculated as 100(A26080°C – A26020°C)/A26020°C] upon duplex formation.
n.d., not determined.