Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation
Abstract Deoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing chemical reactions. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme to be evolved and possesses clinical and biotechnical applications as a biosensor and a knockdown agent. DNAzymes do not require the re...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-06-01
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| Series: | Communications Chemistry |
| Online Access: | https://doi.org/10.1038/s42004-023-00924-3 |
| _version_ | 1827928777199452160 |
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| author | Evan R. Cramer Sarah A. Starcovic Rebekah M. Avey Ali I. Kaya Aaron R. Robart |
| author_facet | Evan R. Cramer Sarah A. Starcovic Rebekah M. Avey Ali I. Kaya Aaron R. Robart |
| author_sort | Evan R. Cramer |
| collection | DOAJ |
| description | Abstract Deoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing chemical reactions. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme to be evolved and possesses clinical and biotechnical applications as a biosensor and a knockdown agent. DNAzymes do not require the recruitment of other components to cleave RNA and can turnover, thus they have a distinct advantage over other knockdown methods (siRNA, CRISPR, morpholinos). Despite this, a lack of structural and mechanistic information has hindered the optimization and application of the 10-23 DNAzyme. Here, we report a 2.7 Å crystal structure of the RNA-cleaving 10-23 DNAzyme in a homodimer conformation. Although proper coordination of the DNAzyme to substrate is observed along with intriguing patterns of bound magnesium ions, the dimer conformation likely does not capture the true catalytic form of the 10-23 DNAzyme. |
| first_indexed | 2024-03-13T06:13:30Z |
| format | Article |
| id | doaj.art-580d77483d534dbcbed32b06bc3ea6b9 |
| institution | Directory Open Access Journal |
| issn | 2399-3669 |
| language | English |
| last_indexed | 2024-03-13T06:13:30Z |
| publishDate | 2023-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Chemistry |
| spelling | doaj.art-580d77483d534dbcbed32b06bc3ea6b92023-06-11T11:07:43ZengNature PortfolioCommunications Chemistry2399-36692023-06-01611610.1038/s42004-023-00924-3Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformationEvan R. Cramer0Sarah A. Starcovic1Rebekah M. Avey2Ali I. Kaya3Aaron R. Robart4Department of Biochemistry and Molecular Medicine, West Virginia UniversityDepartment of Biochemistry and Molecular Medicine, West Virginia UniversityDepartment of Biochemistry and Molecular Medicine, West Virginia UniversityNE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National LaboratoryDepartment of Biochemistry and Molecular Medicine, West Virginia UniversityAbstract Deoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing chemical reactions. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme to be evolved and possesses clinical and biotechnical applications as a biosensor and a knockdown agent. DNAzymes do not require the recruitment of other components to cleave RNA and can turnover, thus they have a distinct advantage over other knockdown methods (siRNA, CRISPR, morpholinos). Despite this, a lack of structural and mechanistic information has hindered the optimization and application of the 10-23 DNAzyme. Here, we report a 2.7 Å crystal structure of the RNA-cleaving 10-23 DNAzyme in a homodimer conformation. Although proper coordination of the DNAzyme to substrate is observed along with intriguing patterns of bound magnesium ions, the dimer conformation likely does not capture the true catalytic form of the 10-23 DNAzyme.https://doi.org/10.1038/s42004-023-00924-3 |
| spellingShingle | Evan R. Cramer Sarah A. Starcovic Rebekah M. Avey Ali I. Kaya Aaron R. Robart Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation Communications Chemistry |
| title | Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation |
| title_full | Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation |
| title_fullStr | Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation |
| title_full_unstemmed | Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation |
| title_short | Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation |
| title_sort | structure of a 10 23 deoxyribozyme exhibiting a homodimer conformation |
| url | https://doi.org/10.1038/s42004-023-00924-3 |
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