Haldar, Susanta;
Zhang, Yashu;
Xia, Ying;
Islam, Barira;
Liu, Sisi;
Gervasio, Francesco L;
Mulholland, Adrian J;
... Haider, Shozeb; + view all
(2021)
Ligand-induced unfolding mechanism of an RNA G-quadruplex.
BioRxiv: Cold Spring Harbor, NY, USA.
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Abstract
The cationic porphyrin, TMPyP4, is a well-established DNA G-quadruplex (G4) binding ligand that can stabilize different topologies via multiple binding modes. However, TMPyP4 has completely opposite destabilizing and unwinding effect on RNA G4 structures. The structural mechanisms that mediate RNA G4 unfolding remains unknown. Here, we report on the TMPyP4-induced RNA G4 unfolding mechanism studied by well-tempered metadynamics (WT-MetaD) with supporting biophysical experiments. The simulations predict a two-state mechanism of TMPyP4 interaction via a groove-bound and a top-face bound conformation. The dynamics of TMPyP4 stacking on the top tetrad disrupts Hoogsteen H-bonds between guanine bases resulting in the consecutive TMPyP4 intercalation from top-to-bottom G-tetrads. The results reveal a striking correlation between computational and experimental approaches and validate WT-MetaD simulations as a powerful tool for studying RNA G4-ligand interactions.
| Type: | Working / discussion paper |
|---|---|
| Title: | Ligand-induced unfolding mechanism of an RNA G-quadruplex |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1101/2021.10.26.465985 |
| Publisher version: | https://doi.org/10.1101/2021.10.26.465985 |
| Language: | English |
| Additional information: | The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license (http://creativecommons.org/licenses/by-nd/4.0/). |
| UCL classification: | UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > UCL School of Pharmacy > Pharma and Bio Chemistry UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > UCL School of Pharmacy |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10142953 |
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