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c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry

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PETERKOVÁ Kateřina DURNÍK Ivo MAREK Radek PLAVEC Janez PODBEVŠEK Peter

Rok publikování 2021
Druh Článek v odborném periodiku
Časopis / Zdroj Nucleic Acids Research
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
www DOI: 10.1093/nar/gkab659
Doi http://dx.doi.org/10.1093/nar/gkab659
Klíčová slova G-quadruplex; deoxyuridine nucleotide; pyrene; covalent probe; NMR spectroscopy; molecular dynamics
Přiložené soubory
Popis Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interactionwith small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy)into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from pi–pi stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
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