Molecular Recognition of Parallel G-quadruplex [d-(TTGGGGT)]₄ Containing Tetrahymena Telomeric DNA Sequence by Anticancer Drug Daunomycin: NMR-Based Structure and Thermal Stability.

Ritu Barthwal,Zia Tariq

doi:10.3390/molecules23092266

Ritu Barthwal, Zia Tariq

Open Access

https://doi.org/10.3390/molecules23092266

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Abstract

The anticancer drug daunomycin exerts its influence by multiple strategies of action to interfere with gene functioning. Besides inhibiting DNA/RNA synthesis and topoisomerase-II, it affects the functional pathway of telomere maintenance by the telomerase enzyme. We present evidence of the binding of daunomycin to parallel-stranded tetramolecular [d-(TTGGGGT)]4 guanine (G)-quadruplex DNA comprising telomeric DNA from Tetrahymena thermophilia by surface plasmon resonance and Diffusion Ordered SpectroscopY (DOSY). Circular Dichroism (CD) spectra show the disruption of daunomycin dimers, suggesting the end-stacking and groove-binding of the daunomycin monomer. Proton and phosphorus-31 Nuclear Magnetic Resonance (NMR) spectroscopy show a sequence-specific interaction and a clear proof of absence of intercalation of the daunomycin chromophore between base quartets or stacking between G-quadruplexes. Restrained molecular dynamics simulations using observed short interproton distance contacts depict interaction at the molecular level. The interactions involving ring A and daunosamine protons, the stacking of an aromatic ring of daunomycin with a terminal G6 quartet by displacing the T7 base, and external groove-binding close to the T1–T2 bases lead to the thermal stabilization of 15 °C, which is likely to inhibit the association of telomerase with telomeres. The findings have implications in the structure-based designing of anthracycline drugs as potent telomerase inhibitors.

Highlights

Guanine (G) repetitive DNA form a four-stranded non-canonical G-quadruplex DNA structure by Hoogsteen hydrogen bonding
Long telomeric sequences usually exist in several conformations involving range between 30–960 μM (Figure 2b), indicating that a specific interaction of daunomycin with [ddifferent (TTGGGGT)]
The present study focuses on the binding of daunomycin to parallel-stranded tetramolecular

Summary

Introduction

Guanine (G) repetitive DNA form a four-stranded non-canonical G-quadruplex DNA structure by Hoogsteen hydrogen bonding. The folding of single-stranded telomeric DNA into a quadruplex structure inhibits telomerase enzyme, affecting cell death by apoptosis pathways. Guanine-rich sequences are located in many other biologically significant regions of genomes, such as promoters of oncogenes (e.g., c-kit, c-myc, bcl-2), recombination hot spots, 50 UTR regions, immunoglobulin switch regions; and are correlated with gene expression [3]. Ligands that bind to G-quadruplex and stabilize its structure interfere with telomerase function, oncogene expression, and genomic stability. This has since evolved as an effective strategy and paved the way for the discovery of novel small molecules/ligands that can bind selectively to G-quadruplex DNA. The focus of research in this direction is to understand the Molecules 2018, 23, 2266; doi:10.3390/molecules23092266 www.mdpi.com/journal/molecules

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