Guiding the folding of G-quadruplexes through loop residue interactions

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Biology

Background:

• G-rich sequences can fold into various quadruplex structures.
• Controlling the topology of these structures is crucial for their function.
• Loop regions significantly influence quadruplex stability and conformation.

Purpose of the Study:

• To design and stabilize specific G-rich quadruplex topologies.
• To investigate the role of loop residues in determining topological preferences.
• To understand the structural and thermodynamic basis of quadruplex folding.

Main Methods:

• Design of G-rich sequences with potential for parallel or hybrid topologies.
• Introduction of single and double mutations and loop modifications.
• High-resolution Nuclear Magnetic Resonance (NMR) spectroscopy for structural determination.
• Thermodynamic stability measurements.

Main Results:

• Mutations and loop shortening influenced the topological equilibrium between parallel and hybrid forms.
• Specific modifications were identified to lock the G-rich sequences into desired topologies without significant structural changes.
• Critical loop residue interactions were elucidated through structural and thermodynamic analyses.
• A conserved stabilizing stacking interaction involving the last residue of a lateral loop was identified.
• Single-nucleotide loops were shown to favor all-parallel topologies.

Conclusions:

• Detailed structural and thermodynamic insights into loop interactions in G-rich quadruplexes.
• Understanding these interactions is key for designing artificial quadruplexes for biotechnological applications, including therapeutics.
• The study provides a foundation for engineering G-quadruplexes with tailored properties.