Intramolecular recombination R-triplex in solution: stabilization by bis-intercalator YOYO

Area of Science:

• Molecular Biology
• Biophysics
• Supramolecular Chemistry

Background:

• Recognizing mixed-sequence double-stranded DNA with oligonucleotides is challenging.
• Protein-free DNA triplexes exhibit low stability.
• Bis-intercalators like YOYO offer potential for stabilizing DNA structures.

Purpose of the Study:

• To investigate the thermodynamic properties of YOYO complexes with DNA oligonucleotides.
• To assess the impact of YOYO binding on DNA triplex and hairpin stability.
• To explore the binding stoichiometry of YOYO with DNA structures.

Main Methods:

• Utilized model oligonucleotides R(2AP)CW and CW.
• Employed bis-intercalator YOYO for complex formation.
• Measured thermodynamic characteristics, including fluorescence intensity and melting temperature (Tm) using 2-aminopurine (2AP) fluorescence.
• Investigated YOYO binding in 0.5 M LiCl.

Main Results:

• Each oligonucleotide bound two YOYO molecules via intercalation, increasing fluorescence 40-fold.
• YOYO binding increased the R(2AP)CW triplex melting temperature from 19°C to 33°C.
• Up to five YOYO molecules bound to R(2AP)CW triplex and six to CW hairpin at higher concentrations.

Conclusions:

• Bis-intercalator YOYO can stabilize DNA triplex and hairpin structures.
• YOYO binding enhances the thermal stability of these DNA conformations.
• The study provides thermodynamic insights into YOYO-DNA interactions for potential applications in DNA recognition.