Shedding light on the base-pair opening dynamics of nucleic acids in living human cells

Yudai Yamaoki, Takashi Nagata (), Keiko Kondo, Tomoki Sakamoto, Shohei Takami and Masato Katahira ()
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Yudai Yamaoki: Kyoto University
Takashi Nagata: Kyoto University
Keiko Kondo: Kyoto University
Tomoki Sakamoto: Kyoto University
Shohei Takami: Kyoto University
Masato Katahira: Kyoto University

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: Abstract Base-pair opening is a fundamental property of nucleic acids that plays important roles in biological functions. However, studying the base-pair opening dynamics inside living cells has remained challenging. Here, to determine the base-pair opening kinetics inside living human cells, the exchange rate constant ( $${k}_{{{{{{\rm{ex}}}}}}}$$ k ex ) of the imino proton with the proton of solvent water involved in hairpin and G-quadruplex (GQ) structures is determined by the in-cell NMR technique. It is deduced on determination of $${k}_{{{{{{\rm{ex}}}}}}}$$ k ex values that at least some G-C base pairs of the hairpin structure and all G-G base-pairs of the GQ structure open more frequently in living human cells than in vitro. It is suggested that interactions with endogenous proteins could be responsible for the increase in frequency of base-pair opening. Our studies demonstrate a difference in dynamics of nucleic acids between in-cell and in vitro conditions.

Date: 2022
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DOI: 10.1038/s41467-022-34822-4

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