Studying DNA G-Quadruplex Aptamer by 19 F NMR

ACS Omega
Takumi IshizukaYan Xu

Abstract

In this study, we demonstrated that 19F NMR can be used to study the thrombin-binding aptamer (TBA) DNA G-quadruplex, widely used as a model structure for studying G-quadruplex aptamers. We systematically examined the structural feature of the TBA G-quadruplex aptamer with fluorine-19 (19F) labels at all of the thymidine positions. We successfully observed the structural change between the G-quadruplex and the unstructured single strand by 19F NMR spectroscopy. The thermodynamic parameters of these DNA G-quadruplex aptamers were also determined from the 19F NMR signals. We further showed that the 19F NMR method can be used to observe the complex formed by TBA G-quadruplex and thrombin. Our results suggest that 19F NMR spectroscopy is a useful approach to study the aptamer G-quadruplex structure.

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Citations

Apr 14, 2021·Nucleosides, Nucleotides & Nucleic Acids·Rugiya AlievaElena Zavyalova
Jan 18, 2020·Biochemical and Biophysical Research Communications·Yue MaKazuo Nagasawa
Jan 30, 2020·The Journal of Organic Chemistry·Mikolaj ChrominskiJacek Jemielity

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Methods Mentioned

BETA
NMR
circular dichroism

Software Mentioned

CHARMm
BIOVIA Discovery Studio

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