Investigation into G4–Ligand Complex in Living Human Cells Using In-cell NMR Spectroscopy

Daniel Krafčík^1,3,*, Michaela Krafčíková², Eva Maturová¹, Pavlína Víšková¹, Kateřina Beková¹, Silvie Foldynová-Trantírková^1,2, Lukáš Trantírek¹

¹Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic

²Institute of Biophysics of the AS CR, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic

³National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic

* krafcik.daniel@gmail.com

Recently, we established an in-cell NMR based approach for monitoring of interactions between double-stranded DNA targets and low molecular weight compounds (ligands) in living human cells^1,2. The method relies on the acquisition of NMR data from cells electroporated either with preformed DNA-ligand complexes or by incubation of electroporated cells with given ligand. 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.

Here, we report how the interactions of chosen examples of G-quadruplex DNA and G-quadruplex binding ligands from the study can be monitored by using the in-cell NMR. This comparative study is based on the data from in vitro measurements, interactions of the complex in the environment of the crude lysate and the in-cell NMR experiments. Our data suggest that in-cell NMR can be used to assess selectivity of G-quadruplex binding ligands with respect to topologically distinct G-quadruplex targets under complex physiological conditions with many times different result than in vitro environment. 

1. Krafcikova, M.; Dzatko, S.; Caron, C., Granzhan, A.; Fiala, R.; Loja, T.; Teulade-Fichou, M.P.; Fessl, T.; Hänsel-Hertsch, R.; Mergny, J.L.; Foldynova-Trantirkova, S.; Trantirek, L.; J. Am. Chem. Soc., 2019, 141, 34, 13281-13285.

2. Viskova, P.; Krafcik, D.; Trantirek, L.; Foldynova-Trantirkova, S.; Curr. Protoc. Nucleic Acid Chem., 2019, 76(1), e71.

This research was supported by the grant from Czech Science Foundation (19-26041X), by the grant from Ministry of Health of the Czech Republic (NV19-08-00450), and by the project SYMBIT (CZ.02.1.01/0.0/0.0/15_003/0000477) funded by the European Regional Development Fund and Ministry of Education, Youth, and Sports (MEYS) of the Czech Republic. MEYS is also acknowledged for its support of access to research infrastructure (CEITEC 2020 LQ1601; CIISB-LM2018127; Czech-BioImaging LM2018129; EATRIS-CZ LM2018133).