pH-driven conformational switch between non-canonical DNA structures in a C-rich domain of EGFR promoter

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Epidermal Growth Factor Receptor (EGFR) is a key oncogene implicated in various human cancers.
• Dysregulation of EGFR signaling pathways necessitates targeted therapeutic interventions, such as tyrosine kinase inhibitors.
• A G-rich domain in the EGFR promoter, previously shown to form G-quadruplex structures, is a critical regulatory element.

Purpose of the Study:

• To investigate the structural properties of the C-rich strand (EGFR-272_C) complementary to the EGFR promoter's G-rich domain.
• To determine if EGFR-272_C can form non-canonical DNA structures, specifically an i-motif.
• To assess the potential of these structures as novel therapeutic targets in EGFR-driven cancers.

Main Methods:

• Circular Dichroism (CD) spectroscopy to analyze DNA secondary structures.
• Nuclear Magnetic Resonance (NMR) spectroscopy for detailed structural elucidation.
• Gel electrophoresis to study DNA structural transitions under varying conditions (pH, salt, co-solvent).

Main Results:

• The EGFR-272_C strand was demonstrated to form an intramolecular i-motif (iM) structure.
• The iM formation is dependent on experimental conditions, coexisting with a hairpin structure.
• The identified iM structure competes with standard DNA duplex formation.

Conclusions:

• The EGFR promoter's C-rich strand can form an i-motif structure, representing a novel regulatory mechanism.
• This i-motif structure presents a potential new target for anticancer drug development.
• Preliminary studies identified phenanthroline derivatives as potential binders to the i-motif structure.