Probing intracellular folding and dynamics of telomeric DNA structures with single-molecule FRET

Project Information

G4invivo

Grant agreement ID: 661415

DOI

10.3030/661415

Project closed

EC signature date 27 March 2015

Start date 1 January 2016

End date 31 December 2017

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 212 194,80

EU contribution

€ 212 194,80

Coordinated by

AARHUS UNIVERSITET
Denmark

Periodic Reporting for period 1 - G4invivo (Probing intracellular folding and dynamics of telomeric DNA structures with single-molecule FRET)

Reporting period: 2016-01-01 to 2017-12-31

Summary of the context and overall objectives of the project

Non-canonical DNA secondary structures can participate in several biological processes, such as transcription, replication and telomere lengthening, etc. G-quadruplexes are examples of such non-canonical DNA structures that, in particular, are expected to occur at telomeres and gene promoters regions of the human genome. Several recent observations strongly support the occurrence and functional relevance of G-quadruplexes in vivo, however a detailed description of their behaviour under cellular conditions is currently missing. Their investigation under physiological settings is important in order to understand the mechanisms of their action at the cellular level and furthermore use them as potential drug targets.
Telomeric G-quadruplexes, in particular, are polymorphic and dynamical structures that can form a variety of molecular structures under different experimental conditions. This intrinsic polymorphism and dynamics is difficult to resolve with the majority of classical biophysical techniques that provide both structure and time averaged ensemble results. In order to overcome these complications, we used high-resolution single-molecule fluorescence microscopy techniques. These methods allow probing the behavior of G-quadruplex molecules one by one and thus allow obtaining a direct view of both their structure and dynamics. The objective of the project was to probe the conformation and structural dynamics of G-quadruplex DNA under a range of cell-mimicking milieu to obtain a mechanistic understanding of their behavior.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In this project, we have investigated the behavior of G-quadruplexes under different conditions in a bottom-up approach - starting from physiologically relevant buffers, towards more cell-like conditions introduced by the presence of polymer-based crowding agents and human cell lysates. Our investigations allowed obtaining a direct view of the folding and underlying conformational dynamics of G-quadruplexes in physiological salt solutions. We found that G-quadruplex folding is very complicated and proceeds through a complex multi-route pathway, involving several marginally stable conformational states.
We could also directly follow the ligand binding to individual G-quadruplex structures and identified two important mechanisms that are determinant to G-quadruplex-ligand interactions: ligand-induced G-quadruplex folding and ligand trapping of transiently folded structures.
Our experiments in molecularly crowded solutions indicate that crowding significantly affects the folding dynamics of G-quadruplexes. Importantly, we find that under near physiological conditions (crowding levels >25 %) G-quadruplexes are expected to be largely stabilized, which points towards the fact that G-quadruplexes are likely to be folded inside cells.
In addition, we have developed new protocols for preparation of cell extracts suitable for single-molecule experiments. Based on our single-molecule experiments in cell extracts we find that the proteins present in cell extracts affect the G-quadruplex folding.
Thus, our experiments established a global view of the behaviour of human telomeric G-quadruplexes under broad experimental conditions, bridging the dilute aqueous solutions and molecularly crowded cellular environments. Altogether, we find that under cellular level the behaviour of G-quadruplexes will be determined and fine-tuned by the combination of the effect of excluded volume due to high levels of cellular crowding and direct specific protein-DNA interactions.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project provides a direct and integrated view of the behaviour of G-quadruplexes in physiologically relevant milieux that will greatly enhance our understanding of these important biological molecules. The results of this project provide new opportunities to design novel and alternative anti-cancer therapies using G-quadruplex structures as drug targets. They can be used by specialists interested in either the chemistry and/or biology of these systems as well as by medical specialists that can potentially use these structures as targets for pharmacological intervention.

Folding dynamics of human telomeric G-quadruplexes. Adapted from Aznauryan et al. NAR 2016