Effect of loop orientation on quadruplex-TMPyP4 interaction.

Area of Science:

• Biochemistry and Molecular Biology
• Medicinal Chemistry
• Genomics

Background:

• G-quadruplexes are DNA structures with therapeutic potential, driving interest in small molecule interactions.
• Genome sequencing reveals numerous G-quadruplex forming sequences, highlighting their biological relevance.
• Ligand binding to G-quadruplexes is influenced by their conformation, particularly loop orientation.

Purpose of the Study:

• To investigate the interaction of the G-quadruplex binding ligand TMPyP4 with DNA quadruplexes of varying loop orientations.
• To elucidate how differences in G-quadruplex loop structure affect molecular recognition by small molecules.
• To compare the binding affinity and modes of TMPyP4 with parallel and antiparallel G-quadruplexes and duplex DNA.

Main Methods:

• UV-Vis spectroscopy
• Isothermal Titration Calorimetry (ITC)
• Surface Plasmon Resonance (SPR) studies
• Synthesis and characterization of TMPyP4 and DNA quadruplex models.

Main Results:

• TMPyP4 exhibits significantly higher binding affinity for parallel G-quadruplexes (c-myc, c-kit) compared to antiparallel human telomeric G-quadruplex.
• Binding affinity for parallel quadruplexes was approximately 10^7 M^-1, while for antiparallel it was around 10^4 M^-1.
• TMPyP4 demonstrated two binding modes with parallel quadruplexes (end-stacking and external binding) and one mode with duplex DNA.

Conclusions:

• G-quadruplex loop orientation dictates distinct conformations, critically influencing small molecule binding.
• TMPyP4 shows a strong preference for parallel G-quadruplex structures, suggesting conformational selectivity in ligand-DNA interactions.
• Understanding these structure-affinity relationships is crucial for designing targeted G-quadruplex-based therapeutics.