Dynamic Structures and Fast Transition Kinetics of Oxidized G-Quadruplexes

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Oxidative stress can damage DNA, leading to modified bases like 8-oxoguanine (8-oxoG).
• 8-oxoG can alter the structure and function of G-rich DNA sequences, including G-quadruplexes (GQs).
• Cellular environments are molecularly crowded, influencing DNA structure and interactions.

Purpose of the Study:

• To investigate the structural stability and ligand binding properties of oxidized human telomeric G-quadruplexes (GQs) in a simulated crowded cellular environment.
• To understand how molecular crowding and 8-oxoguanine modification affect GQ formation cooperativity with platinum (Pt(II)) binders.

Main Methods:

• Mimicking cellular crowding using 40% DMSO or sucrose.
• Stability assays of wild-type (WT) and oxidized GQs.
• Investigating Pt(II) binder cooperativity under crowded conditions.
• Single-molecule mechanical unfolding to analyze GQ structural dynamics and folding kinetics.

Main Results:

• Oxidized human telomeric GQs exhibit stabilities comparable to WT GQs in crowded conditions.
• While WT GQs show negative cooperativity with Pt(II) binders in crowding, oxidized GQs display positive cooperativity.
• Single-molecule unfolding reveals oxidized GQs form more diverse, flexible structures with faster kinetics, enabling preferential Pt(II) binding.

Conclusions:

• Oxidized G-rich structures in crowded environments exhibit unique folding dynamics and altered ligand binding cooperativity.
• These findings enhance understanding of DNA structure and gene regulation under oxidative stress.
• Provides insights for designing targeted ligands for oxidized DNA structures relevant to cellular oxidative stress.