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

AutorEritja Casadellà, Ramón; Murphy, Deirdre Brendan; Doyle, Hugh; Redmond, Gareth
Palabras claveoligonucleotide
absorption spectrophotometry
base mispairing
molecular stability
temperature dependence
Thermodynamics
Oligodeoxyribonucleotides
Ultraviolet
Fecha de publicaciónoct-2004
EditorAdenine Press
CitaciónJournal of Biomolecular Structure and Dynamics
ResumenThree-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 kcal/mol. The influence of a mispaired base in these systems is shown to destabilize a nick complex by 3.1 kcal/mol and a gap complex by 2.8 kcal/mol, respectively.
Versión del editorhttp://www.tandfonline.com/doi/abs/10.1080/07391102.2004.10506995
URIhttp://hdl.handle.net/10261/124866
E-ISSN07391102
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