Thermodynamic comparison of PNA/DNA and DNA/DNA hybridization reactions at ambient temperature

• Published in: Nucleic acids research 1999-12, Vol.27 (24), p.4792-4800
• Main Authors: Schwarz, Frederick P., Robinson, Scott, Butler, John M.
• Format: Article
• Language: English
• Subjects: Base Sequence; Calorimetry - methods; DNA - chemistry; Nucleic Acid Denaturation; Nucleic Acid Hybridization; Oligodeoxyribonucleotides - chemistry; Peptide Nucleic Acids - chemistry; Thermodynamics
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/27.24.4792

The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5′-ATGCXYATGC-3′ with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the binding constants range from 1.8 × 106 M−1 for PNA(TT)/DNA to 4.15 × 107 M−1 for PNA(GA)/DNA and the binding enthalpies range from −194 kJ mol−1 for PNA(CG)/DNA to −77 kJ mol−1 for PNA(GT)/DNA. For the corresponding DNA/DNA binding reactions, the binding constants range from 2.9 × 105 M−1 for DNA(GT)/DNA to 1.9 × 107 M−1 for DNA(CC)/DNA and the binding enthalpies range from −223 kJ mol−1 for DNA(CG)/DNA to −124 kJ mol−1 for DNA(TT)/DNA. Most of the PNA sequences exhibited tighter binding affinities than their corresponding DNA sequences resulting from smaller entropy changes in the PNA/DNA hybridization reactions. van't Hoff enthalpies and extrapolated ΔG values determined from UV melting studies on the duplexes exhibited closer agreement with the ITC binding enthalpies and ΔG values for the DNA/DNA duplexes than for the PNA/DNA duplexes.