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2024 | Book

Metal-Responsive Base Pair Switching of Ligand-type Uracil Nucleobases

Author: Keita Mori

Publisher: Springer Nature Singapore

Book Series : Springer Theses

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About this book

In this thesis, the author proposes "metal-responsive base pair switching" of ligand-modified nucleobases as a novel tool for stimuli-responsive control of DNA assemblies. It is written to demonstrate broad applicability of the base pair switching in dynamic DNA nanotechnology and inspire researchers to use this technique. Based on specific interactions between ligand-type nucleobases and target metal ions, in this volume, DNA hybridization was dynamically controlled through strand displacement reactions. The base pair switching was further applied to develop metal-dependent DNA molecular machines. This novel strategy for stimuli-responsive regulation of DNA assemblies will greatly expand the scope of dynamic DNA nanotechnology. This volume uniquely features importance of elaborate molecular design based on chemistry for imparting stimuli responsiveness to DNA assemblies.

Table of Contents

Frontmatter
Chapter 1. General Introduction
Abstract
Sequence-dependent self-assembly of DNA molecules has been used to develop advanced nanoarchitectures, giving rise to “DNA nanotechnology”. Since Seeman et al. reported branched DNA assemblies, methodologies for fabricating DNA nanostructures have been developed dramatically, represented by DNA origami technique. Dynamic conversion of DNA structures has also been achieved based on strand displacement reactions (SDRs), resulting in DNA-based molecular machines and nanodevices operated by specific sequences of oligonucleotides. Recently, it has gained much attention to construct DNA systems driven by external stimuli instead of nucleic acid strands. In particular, metal ions show unique properties such as reversible complexation, stimuli-responsiveness, and binding specificity. This chapter overviews the history of DNA nanotechnology spanning from early studies of DNA nanostructures to recent examples of dynamic DNA nanodevices. Stimuli-responsive DNA systems are also highlighted, focusing on characteristics of each stimulus. In particular, metal-mediated base pairing is discussed as a strategy for metal-responsive control of DNA assemblies.
Keita Mori
Chapter 2. Metal-Responsive DNA Strand Displacement Reactions Driven by Base Pair Switching of 5-Hydroxyuracil Nucleobases
Abstract
Toehold-mediated DNA strand displacement reactions (SDRs) are an essential tool for the construction of DNA-based molecular machines. In this chapter, I demonstrated “base pair switching” of 5-hydroxyuracil (UOH) bases and applied it for metal-responsive SDRs. The UOH bases were known to form both hydrogen-bonded UOH–A pairs and metal-mediated UOH–GdIIIUOH pairs. Therefore, it was expected that the base-pairing partner of UOH can be switched from A to UOH by the addition of GdIII ions, resulting in metal-responsive base pair switching. UV melting analysis revealed that the order of thermal stability was inverted among two UOH-containing duplexes, one with UOH–A pairs and the other with UOHUOH mismatches, by the addition of GdIII ions. This result supported GdIII-responsive base pair switching from UOH–A to UOH–GdIIIUOH, which was utilized for metal-responsive SDRs. According to time-course fluorescence measurement, the addition of GdIII ions triggered the SDR from the duplex containing UOH–A pairs to that with UOH–GdIIIUOH pairs. The SDR driven by the base pair switching of UOH will be a powerful tool for developing metal-responsive DNA nanodevices.
Keita Mori
Chapter 3. Metal-Dependent Base Pair Switching of N,N-Dicarboxymethyl-5-Aminouracil Nucleosides
Abstract
The base pair switching of UOH has had limited application because it requires the consecutive introduction of multiple UOH bases into DNA strands. In this chapter, I aimed to develop metal-responsive base pair switching by a singly incorporated ligand-type nucleobase. To this end, I designed N,N-dicarboxymethyl-5-aminouracil (dcaU) containing an iminodiacetate ligand. The dcaU base was expected to show higher coordination ability than UOH due to its negative charges and chelate effects. After obtaining dcaU phosphoramidite, dcaU-containing DNA strands were synthesized by an automated DNA synthesizer. In the presence of GdIII ions, a DNA duplex with a dcaUdcaU pair was significantly stabilized due to the formation of dcaU–GdIIIdcaU pairs. As a result, the addition of GdIII ions reversed the relative stability of two duplexes containing dcaU–A or dcaUdcaU pairs, indicating base pair switching between dcaU–A and dcaU–GdIIIdcaU. The base pair switching of dcaU was further applicable for GdIII-responsive DNA strand exchange. These results showed that the efficiency of the base pair switching can be rationally controlled by careful design of ligand-type nucleobases.
Keita Mori
Chapter 4. Metal-Responsive DNA Tweezers Driven by Base Pair Switching of 5-Hydroxyuracil Nucleobases
Abstract
Controlling DNA nanomachines in response to metal ions will broadly extend their functions and rate of operation. In this chapter, I operated DNA tweezers by metal-responsive base pair switching of UOH bases. A pair of DNA tweezers was designed to be closed by hybridization of a UOH-containing closing strand through UOH–A pairing. The addition of GdIII ions was expected to destabilize the UOH–A pairs and release the closing strand with the UOH–GdIIIUOH complexes, opening the tweezers. Native polyacrylamide gel electrophoresis revealed that the UOH-modified tweezers were predominantly closed (66%) in the absence of GdIII ions. On the other hand, the addition of GdIII released the UOH-containing closing strand along with UOH–GdIIIUOH complexes, opening 83% of the tweezers. The GdIII-dependent structural conversion was also proven by fluorescence analysis using tweezers with a pair of fluorophore and quencher. Furthermore, the UOH-modified tweezers were reversibly operated by the addition and removal of GdIII ions under isothermal conditions. These results demonstrated that the base pair switching of UOH would be widely applicable to metal-responsive operation of DNA molecular machines.
Keita Mori
Chapter 5. Conclusion
Abstract
In this study, coordination-driven base pair switching of modified uracil bases was proposed and applied to dynamic control of DNA structures. DNA strand displacement reactions essential for DNA structural conversion were successfully controlled in a GdIII-responsive manner by introducing 5-hydroxyuracil (UOH) bases at the termini of DNA strands. To resolve the sequence limitation of the UOH bases, an N,N-dicarboxymethyl-5-aminouracil (dcaU) base with an iminodiacetate ligand was developed and the GdIII-dependent base pair switching was achieved with a single incorporation of dcaU. Finally, it was demonstrated that UOH-modified DNA tweezers were reversibly opened and closed upon addition and removal of GdIII ions, respectively, under isothermal conditions. The introduction of modified uracil bases instead of natural T bases has little effect on the thermal stability and structures of DNA assemblies. Therefore, metal-responsive base pair switching is expected to be widely applicable to the dynamic control of DNA supramolecules. This chapter summarizes the achievements of this study and overviews future perspectives of the “base pair switching” technology.
Keita Mori
Backmatter
Metadata
Title
Metal-Responsive Base Pair Switching of Ligand-type Uracil Nucleobases
Author
Keita Mori
Copyright Year
2024
Publisher
Springer Nature Singapore
Electronic ISBN
978-981-9994-00-7
Print ISBN
978-981-9993-99-4
DOI
https://doi.org/10.1007/978-981-99-9400-7

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