An approach to predicting the stabilities of peptide nucleic acid:DNA duplexes

An approach is described for predicting peptide nucleic acid (PNA):DNA duplex stability from base sequence by approximating the total free energy of dissociation, delta G degree tot, for these duplexes as the sum of five parameters: (a) a nearest-neighbor interaction summation term, sigma Nj delta G degree j; (b) an initiation term, delta G degree i; (c) a dangling-end stabilization term, delta G degree e; (d) a PNA:DNA stabilization term per nearest-neighbor interaction, delta G degree pna; and (e) an ionic strength term, delta G degree Na. Parameters (a) and (b) are approximated using previously determined values for DNA:DNA duplexes, whereas parameters (c), (d), and (e) are empirically determined. These terms are used to calculated delta G degree tot, which is used in conjunction with a transition enthalpy (delta H degree) value, also approximated from nearest-neighbor values previously derived for DNA:DNA duplexes, to calculate a melting temperature (Tm) for the PNA:DNA duplex. Predicted Tm values calculated by this approach agreed fairly well with measured values for 11 different PNA:DNA duplexes, as well as with literature values. The approach also accurately models ionic strength effects.