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

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Ionic liquid induced G-quadruplex formation and stabilization: spectroscopic and simulation studies.

Sagar Satpathi¹, Mandar Kulkarni¹, Arnab Mukherjee¹

¹Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India. p.hazra@iiserpune.ac.in arnab.mukherjee@iiserpune.ac.in.

Physical Chemistry Chemical Physics : PCCP

|November 3, 2016

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Ionic liquids can now form and stabilize G-quadruplex (GQ) DNA structures, crucial for cellular aging and cancer research. This discovery offers new avenues for designing novel GQ stabilizers.

Area of Science:

Biochemistry
Molecular Biology
Materials Science

Background:

G-quadruplex (GQ) DNA structures are vital in cellular processes like aging and cancer.
Conventional stabilizers for GQ formation include small ions like Na+, K+, and NH4+.

Purpose of the Study:

To investigate the potential of a specific ionic liquid (IL) as a G-quadruplex (GQ) stabilizer.
To explore the mechanism of GQ formation and stabilization induced by this IL.

Main Methods:

Spectroscopic techniques were employed to confirm conformational changes.
Molecular dynamics (MD) simulations were used to elucidate the interaction between the IL and GQ structures.

Main Results:

The ionic liquid, guanidinium tris(pentafluoroethyl)trifluorophosphate, successfully induced and stabilized GQ formation without conventional ions.

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MD simulations revealed that guanidinium cations interact with the G-tetrad core, while anions associate with the GQ surface.

Conclusions:

This study introduces a novel class of ionic liquids capable of forming and stabilizing G-quadruplex structures.
The findings provide insights for designing future ILs for targeted GQ formation and stabilization applications.