Murphy, D. and Doyle, H. and Eritja, R. and Redmond, G.

2004

Journal Of Biomolecular Structure & Dynamics

Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: A spectroscopic study

Validated

()

22

2

195

203

Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches is monitored using temperature-dependent optical absorption spectroscopy. A sequential three-state equilibrium model is used to analyze the measured melting profiles and evaluate thermodynamic parameters associated with dissociation of the complexes. The free-energy of stabilization of a nick complex compared to a gap complex due to base stacking is determined to be -1.9 kcaUmol. The influence of a mispaired base in these systems is shown to destabilize a nick complex by 3.1 kcaUmol and a gap complex by 2.8 kcal/mol, respectively.

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