Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases

Yusuke Takezawa (), Keita Mori, Wei-En Huang, Kotaro Nishiyama, Tong Xing, Takahiro Nakama and Mitsuhiko Shionoya ()
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Yusuke Takezawa: The University of Tokyo
Keita Mori: The University of Tokyo
Wei-En Huang: The University of Tokyo
Kotaro Nishiyama: The University of Tokyo
Tong Xing: The University of Tokyo
Takahiro Nakama: The University of Tokyo
Mitsuhiko Shionoya: The University of Tokyo

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: Abstract Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated by specific chemical inputs. Herein, we demonstrate the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner. The 5-hydroxyuracil (UOH) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded UOH–A base pair and a metal-mediated UOH–GdIII–UOH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between UOH–A and UOH–GdIII–UOH. Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating UOH bases into the sequence. The metal-mediated base-pair switching will become a versatile strategy for constructing stimuli-responsive DNA nanostructures, expanding the scope of dynamic DNA nanotechnology.

Date: 2023
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DOI: 10.1038/s41467-023-40353-3

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