Issue 5, 2023

Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

Abstract

Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU–GdIIIdcaU pair significantly stabilized the DNA duplex containing one dcaUdcaU mismatch (ΔTm = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU–A pair was destabilized in the presence of GdIIITm = −3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.

Graphical abstract: Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

Supplementary files

Article information

Article type
Edge Article
Submitted
28 Nov 2022
Accepted
02 Jan 2023
First published
03 Jan 2023
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2023,14, 1082-1088

Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

K. Mori, Y. Takezawa and M. Shionoya, Chem. Sci., 2023, 14, 1082 DOI: 10.1039/D2SC06534G

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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