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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

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Published on: April 4, 2025

Molecular crowding promotes the aggregation of parallel structured G-quadruplexes.

Chao Gao¹, Jieya Deng¹, Naureen Anwar²

¹National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.

International Journal of Biological Macromolecules

|April 16, 2023

Summary

Molecular crowding did not induce parallel G-quadruplex formation in model sequences but promoted aggregation. It also inhibited ligand binding to parallel G-quadruplexes, impacting anticancer drug design.

Keywords:

A looser structure Aggregation Molecular crowding Parallel structured G-quadruplexes

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Area of Science:

Biochemistry
Molecular Biology
Medicinal Chemistry

Background:

G-quadruplexes are vital DNA and RNA structures involved in cellular processes.
Intracellular molecular crowding influences G-quadruplex conformation, particularly telomeric structures.
Parallel G-quadruplexes in promoter regions and mRNA are key drug targets, necessitating studies under crowding.

Purpose of the Study:

To investigate the effect of molecular crowding on parallel G-quadruplex structures (c-KIT1, c-MYC, 32KRAS) and their ligand interactions.
To simulate intracellular crowding using polyethylene glycol (PEG200).
To provide insights for designing anticancer drugs targeting parallel G-quadruplexes.

Main Methods:

Circular dichroism (CD) spectral scanning.
Fluorescence resonance energy transfer (FRET).
Native polyacrylamide gel electrophoresis (PAGE).

Main Results:

Molecular crowding did not induce parallel G-quadruplex formation in model sequences but promoted aggregation and looser monomer structures.
Telomeric G-rich sequences formed antiparallel G-quadruplexes under crowding without K+.
Crowding did not change ligand binding stoichiometry to c-KIT1 but inhibited interaction with parallel G-quadruplexes.

Conclusions:

Molecular crowding has complex effects on G-quadruplex structures and ligand interactions.
Crowding conditions do not favor parallel G-quadruplex formation in the studied model sequences.
Findings are crucial for developing targeted anticancer therapies involving parallel G-quadruplexes.