Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases
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, w...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-08-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-40353-3 |
| _version_ | 1797558313743810560 |
|---|---|
| author | Yusuke Takezawa Keita Mori Wei-En Huang Kotaro Nishiyama Tong Xing Takahiro Nakama Mitsuhiko Shionoya |
| author_facet | Yusuke Takezawa Keita Mori Wei-En Huang Kotaro Nishiyama Tong Xing Takahiro Nakama Mitsuhiko Shionoya |
| author_sort | Yusuke Takezawa |
| collection | DOAJ |
| description | 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 (U OH ) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded U OH –A base pair and a metal-mediated U OH –GdIII–U OH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between U OH –A and U OH –GdIII–U OH . Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating U OH 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. |
| first_indexed | 2024-03-10T17:28:29Z |
| format | Article |
| id | doaj.art-75bd2b2cbf284fe9b88fd3722d94aa50 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-10T17:28:29Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-75bd2b2cbf284fe9b88fd3722d94aa502023-11-20T10:05:18ZengNature PortfolioNature Communications2041-17232023-08-0114111010.1038/s41467-023-40353-3Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobasesYusuke Takezawa0Keita Mori1Wei-En Huang2Kotaro Nishiyama3Tong Xing4Takahiro Nakama5Mitsuhiko Shionoya6Department of Chemistry, Graduate School of Science, The University of TokyoDepartment of Chemistry, Graduate School of Science, The University of TokyoDepartment of Chemistry, Graduate School of Science, The University of TokyoDepartment of Chemistry, Graduate School of Science, The University of TokyoDepartment of Chemistry, Graduate School of Science, The University of TokyoDepartment of Chemistry, Graduate School of Science, The University of TokyoDepartment of Chemistry, Graduate School of Science, The University of TokyoAbstract 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 (U OH ) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded U OH –A base pair and a metal-mediated U OH –GdIII–U OH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between U OH –A and U OH –GdIII–U OH . Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating U OH 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.https://doi.org/10.1038/s41467-023-40353-3 |
| spellingShingle | Yusuke Takezawa Keita Mori Wei-En Huang Kotaro Nishiyama Tong Xing Takahiro Nakama Mitsuhiko Shionoya Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases Nature Communications |
| title | Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases |
| title_full | Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases |
| title_fullStr | Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases |
| title_full_unstemmed | Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases |
| title_short | Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases |
| title_sort | metal mediated dna strand displacement and molecular device operations based on base pair switching of 5 hydroxyuracil nucleobases |
| url | https://doi.org/10.1038/s41467-023-40353-3 |
| work_keys_str_mv | AT yusuketakezawa metalmediateddnastranddisplacementandmoleculardeviceoperationsbasedonbasepairswitchingof5hydroxyuracilnucleobases AT keitamori metalmediateddnastranddisplacementandmoleculardeviceoperationsbasedonbasepairswitchingof5hydroxyuracilnucleobases AT weienhuang metalmediateddnastranddisplacementandmoleculardeviceoperationsbasedonbasepairswitchingof5hydroxyuracilnucleobases AT kotaronishiyama metalmediateddnastranddisplacementandmoleculardeviceoperationsbasedonbasepairswitchingof5hydroxyuracilnucleobases AT tongxing metalmediateddnastranddisplacementandmoleculardeviceoperationsbasedonbasepairswitchingof5hydroxyuracilnucleobases AT takahironakama metalmediateddnastranddisplacementandmoleculardeviceoperationsbasedonbasepairswitchingof5hydroxyuracilnucleobases AT mitsuhikoshionoya metalmediateddnastranddisplacementandmoleculardeviceoperationsbasedonbasepairswitchingof5hydroxyuracilnucleobases |