Impact of Small Molecules on Intermolecular G-Quadruplex Formation.

Prabesh Gyawali,Sanjaya Abeysirigunawardena,Hamza Balci,Keshav Gc,Kazuo Nagasawa,Yue Ma

doi:10.3390/molecules24081570

Prabesh Gyawali, Sanjaya Abeysirigunawardena + Show 4 more

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https://doi.org/10.3390/molecules24081570

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Abstract

We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.

Highlights

G-quadruplex structures (GQs) have emerged as promising targets for cancer therapy [1,2]or transcription-level [3,4,5] and translation-level [6] gene expression regulation, but they have found use in various biotechnology applications [7]
In order to study the impact of small molecules (SMs) on the intermolecular G-quadruplex (i-GQ) formation, we developed an smFRET assay where i-GQ formation is studied in the absence or presence of SMs
Unlike the L2H2-6OTD and Phen-DC3, which did not result in a significant enhancement of the i-GQ formation in the 2+2 GGG configuration, the PDS resulted in a three-fold enhancement. These results suggested that these SMs either did not facilitate the i-GQ formation in the 2+2 GGG configuration or had a relatively weaker impact, compared to the order of magnitude enhancement observed in the 3+1 GGG configuration

Summary

Introduction

G-quadruplex structures (GQs) have emerged as promising targets for cancer therapy [1,2]or transcription-level [3,4,5] and translation-level [6] gene expression regulation, but they have found use in various biotechnology applications [7]. As physiological relevance and technological potential of GQs became better established, research on identifying and synthesizing small molecules (SMs) that stabilize them, experienced significant progress [8,9,10,11]. Prominence of GQ stabilizing SMs is typically characterized by their specificity to GQs, compared to double-stranded or single-stranded. Of GQs. Pyridostatin (PDS), Phen-DC3, and oxazole telomestatin derivatives (OTD) are some of the prominent SMs in these respects (Figure 1A shows chemical structures of these SMs) [12,13,14,15]. L2H2-6OTD [17], and ∆Tm = 35 ◦ C for PDS [18], have been reported under different ionic conditions (50–150 mM KCl).

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