Related Experiment Video
Updated: Aug 23, 2026

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
Published on: November 21, 2017
Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study
Dierdre Murphy1, Hugh Doyle, Ramon Eritja
1Nanotechnology Group, NMRC, Lee Maltings, Prospect Row, Cork, Ireland.
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.
More Related Videos
11:37Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism
Published on: July 28, 2017
10:52Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters
Published on: May 29, 2026
Related Concept Videos
RNA Stability
Nucleic Acid Structure
DNA Structure
DNA has a double-helix structure. The...
DNA Base Pairing