Table 1.
Binding affinity and sequence selectivity of PNAs by ITC and UV thermal melting.
| PNA/dsRNA | Affinitya | HRP1 | HRP2 | HRP3 | HRP4 | dsDNA |
|---|---|---|---|---|---|---|
| PNA1 (M) | Ka × 106 M−1 | 33 ± 1 | 1.3 ± 0.1 | 1.3 ± 0.1 | 1.2 ± 0.1 | 0.8 ± 0.1b |
| Tm °C | 66.5 ± 0.7 | 36.3 ± 0.4 | 36.8 ± 0.4 | 32.6 ± 0.4 | 35.0 ± 0.3b | |
| PNA2 (T) | Ka × 106 M−1 | 1.9 ± 0.1 | 12 ± 1 | 0.9 ± 0.1 | 0.4 ± 0.1 | 0.9 ± 0.1c |
| Tm °C | 46.4 ± 0.5 | 69.6 ± 0.8 | 35.4 ± 0.4 | 34.6 ± 0.2 | 29.4 ± 0.4c | |
| PNA4 (J) | Ka × 106 M−1 | 11 ± 1 | 1.6 ± 0.4 | 0.9 ± 0.1 | 0.4 ± 0.1 | 0.2 ± 0.1b |
| Tm °C | 60.7 ± 0.6 | 43.8 ± 0.6 | 39.1 ± 0.3 | 35.7 ± 0.5 | 29.7 ± 0.3b |
a
Association constants, Ka × 106 M−1, average of three experiments ± stand. dev., for binding of PNAs to the respective hairpins in 50 mM potassium phosphate buffer (pH 7.4) containing 2 mM MgCl2, 90 mM KCl, 10 mM NaCl at 25 °C. UV thermal melting temperatures, Tm °C, average of five experiments ± stand. dev. measured at 300 nm and 18 μM of each dsRNA (or dsDNA) and PNA in the ITC buffer as above.
b
dsDNA of the same sequence as HRP1.
c
dsDNA of the same sequence as HRP2.