Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy

Journal of the American Chemical Society
Michaela KrafcikovaLukáš Trantirek

Abstract

Studies on DNA-ligand interactions in the cellular environment are problematic due to the lack of suitable biophysical tools. To address this need, we developed an in-cell NMR-based approach for monitoring DNA-ligand interactions inside the nuclei of living human cells. Our method relies on the acquisition of NMR data from cells electroporated with preformed DNA-ligand complexes. The impact of the intracellular environment on the integrity of the complexes is assessed based on in-cell NMR signals from unbound and ligand-bound forms of a given DNA target. This technique was tested on complexes of two model DNA fragments and four ligands, namely, a representative DNA minor-groove binder (netropsin) and ligands binding DNA base-pairing defects (naphthalenophanes). In the latter case, we demonstrate that two of the three in vitro-validated ligands retain their ability to form stable interactions with their model target DNA in cellulo, whereas the third one loses this ability due to off-target interactions with genomic DNA and cellular metabolites. Collectively, our data suggest that direct evaluation of the behavior of drug-like molecules in the intracellular environment provides important insights into the development of DNA-bindi...Continue Reading

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Citations

Sep 23, 2020·Nucleic Acids Research·Thi Quynh Ngoc NguyenAnh Tuân Phan
Mar 8, 2020·Biophysics Reviews·Yudai YamaokiMasato Katahira
Sep 26, 2020·Nucleic Acids Research·Derrick J Y TanAnh Tuân Phan
Oct 29, 2020·Biophysics and Physicobiology·Yudai YamaokiMasato Katahira
Sep 26, 2020·Angewandte Chemie·P BroftHarald Schwalbe
Feb 2, 2021·Nucleic Acids Research·Martina Lenarčič ŽivkovićLukáš Trantírek
Oct 15, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Abdul-Hamid EmwasMariusz Jaremko
Aug 18, 2020·Angewandte Chemie·Alberto CollautoThomas F Prisner
Jun 18, 2021·Chemical Communications : Chem Comm·Tomoki SakamotoMasato Katahira
Jul 3, 2021·International Journal of Molecular Sciences·Daniel KrafčíkLukáš Trantírek
Oct 5, 2021·Acta Crystallographica. Section D, Structural Biology·Enrico LuchinatLucia Banci
Nov 13, 2021·Journal of the American Chemical Society·Xiangfei SongLishan Yao

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