AI Article Synopsis
- Researchers studied how base stacking and mismatches affect the stability of three-strand oligonucleotide complexes.
- They monitored melting behavior using temperature-dependent optical absorption spectroscopy to analyze thermodynamic parameters.
- Findings showed that a nick complex is stabilized more than a gap complex (by -1.9 kcal/mol), but mismatches destabilize both types of complexes (by 3.1 kcal/mol for nick and 2.8 kcal/mol for gap).
Article Abstract
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 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.
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| http://dx.doi.org/10.1080/07391102.2004.10506995 | DOI Listing |
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