Journal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Volume 141, Issue 34, Pages 13281-13285Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jacs.9b03031
Keywords
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Categories
Funding
- Czech Science Foundation [16-10504S, 19-26041X]
- Grant Agency of Masaryk University [MUNI/E/0771/2018]
- iNEXT - Horizon 2020 Programme [653706]
- IDI 2016 project - French National Research Agency [ANR-11-IDEX-0003-02]
- project SYMBIT - European Regional Development Fund [CZ.02.1.01/0.0/15_003/0000477]
- Ministry of Education, Youth, and Sports (MEYS) of the Czech Republic
- [CEITEC 2020 LQ1601]
- [CIISB-LM2015043]
- [Czech-BioImaging LM2015062]
- [EATRIS-CZ LM2015064]
- [CZ.02.1.01/0.0/0.0/15003/0000441]
- [8J18FR001]
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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-binding ligands with desirable biological activity and minimal side effects resulting from off-target binding.
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