Fellow's research: A novel probe provides structural insights into therapeutically important nucleic acid structures

09 Apr 2019

Fellow's research: A novel probe provides structural insights into therapeutically important nucleic acid structures


Dr Srivatsan Seergazhi Gopalan, Senior Fellow

Indian Institute of Science Education and Research (IISER), Pune

In our recently published study, we designed multipurpose nucleoside probes to elucidate dynamics of the structure of the therapeutically important nucleic acid structures, G-quadruplexes.

Nucleic acids, the hereditary material, can also catalyse biochemical reactions and regulate protein synthesis by various mechanisms. To perform these essential cellular functions, apart from their classical structure, the nucleic acids adopt complex but defined architectures composed of structural units like the classical double helix, structures with bulges, and hairpins.

Among these structures, G-quadruplexes, which are formed by guanosine (G)-rich DNA/RNA sequences, have been considered very important for biological processes. The location and presence of G-quadruplex-forming sequences across various species are conserved. Additionally, compelling evidence suggests that these structures regulate the activities of several tumour-causing genes by acting as speed breakers or check dams. Therefore, the development of small molecules that can bind and regulate the activity of these checkpoints has been considered as an alternative means to tackle cancer. However, understanding the geometry adopted by individual G-quadruplex-forming sequences in cells and targeting a specific G-quadruplex structure amongst others in the genome has remained a major challenge. This is because the majority of currently available tools poorly differentiate different G-quadruplex structures and are not suitable for in-cell analysis.

To overcome this limitation, we used an innovative probe design approach to investigate G-quadruplex geometries and their ability to bind to drug-like molecules in cells using a geometry-sensitive dual-app nucleoside probe. The probe is similar to nucleic acid thymine/uracil, which is present in DNA/RNA, but is composed of a small fluorescent label and an NMR isotope, fluorine atom. First, we introduced the dual-app probe into a guanosine-rich human telomeric DNA repeat, which end-caps the chromosomes and protects them from degradation. The nucleoside analogue served as a common probe to distinguish different G-quadruplex structures and to quantify ligand binding to different G-quadruplexes using fluorescence and NMR techniques. Second, we used the fluorine NMR signatures to determine the preferred G-quadruplex structure of the human telomeric overhang in live cells.

This study is an important contribution in the field of nucleic acids as it brings us a step closer to understanding the structure and function of therapeutically important nucleic acids in the native cellular environment.



A dual-app nucleoside probe provides structural insights into the human telomeric overhang in live cells. Sudeshna Manna, Debayan Sarkar, and Seergazhi G. Srivatsan Journal of the American Chemical Society. September 2018

Watch the video summary of the publication here: Tags gone smart!