An Approach to Predicting the Stabilities of Peptide Nucleic Acid:DNA Duplexes

Publisher： Elsevier

ISSN： 0003-2697

Source： Analytical Biochemistry, Vol.260, Iss.1, 1998-06, pp. : 56-63

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Abstract

An approach is described for predicting peptide nucleic acid (PNA):DNA duplex stability from base sequence by approximating the total free energy of dissociation, DeltaGtot, for these duplexes as the sum of five parameters: (a) a nearest-neighbor interaction summation term, NjDeltaGj; (b) an initiation term, DeltaGi; (c) a dangling-end stabilization term, DeltaGe; (d) a PNA:DNA stabilization term per nearest-neighbor interaction, DeltaGpna; and (e) an ionic strength term, DeltaGNa. 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 calculate DeltaGtot, which is used in conjunction with a transition enthalpy (DeltaH) 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. Copyright 1998 Academic Press.