Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics
DNAzyme is a class of DNA molecules that can perform catalytic functions with high selectivity towards specific metal ions. Due to its potential applications for biosensors and medical therapeutics, DNAzyme has been extensively studied to characterize the relationships between its biochemical proper...
| Main Authors: | , , , , |
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| Language: | English |
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MDPI AG
2023-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/2/1212 |
| _version_ | 1797441460931395584 |
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| author | Yiming Zhang Zongzhou Ji Xin Wang Yi Cao Hai Pan |
| author_facet | Yiming Zhang Zongzhou Ji Xin Wang Yi Cao Hai Pan |
| author_sort | Yiming Zhang |
| collection | DOAJ |
| description | DNAzyme is a class of DNA molecules that can perform catalytic functions with high selectivity towards specific metal ions. Due to its potential applications for biosensors and medical therapeutics, DNAzyme has been extensively studied to characterize the relationships between its biochemical properties and functions. Similar to protein enzymes and ribozymes, DNAzymes have been found to undergo conformational changes in a metal–ion–dependent manner for catalysis. Despite the important role the conformation plays in the catalysis process, such structural and dynamic information might not be revealed by conventional approaches. Here, by using the single–molecule fluorescence resonance energy transfer (smFRET) technique, we were able to investigate the detailed conformational dynamics of a uranyl–specific DNAzyme 39E. We observed conformation switches of 39E to a folded state with the addition of Mg<sup>2+</sup> and to an extended state with the addition of UO<sub>2</sub><sup>2+</sup>. Furthermore, 39E can switch to a more compact configuration with or without divalent metal ions. Our findings reveal that 39E can undergo conformational changes spontaneously between different configurations. |
| first_indexed | 2024-03-09T12:23:24Z |
| format | Article |
| id | doaj.art-0a247c5a80304d4aaf334c51fd2feeb3 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T12:23:24Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-0a247c5a80304d4aaf334c51fd2feeb32023-11-30T22:37:02ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-01-01242121210.3390/ijms24021212Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational DynamicsYiming Zhang0Zongzhou Ji1Xin Wang2Yi Cao3Hai Pan4Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, ChinaWenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, ChinaWenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, ChinaWenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, ChinaWenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, ChinaDNAzyme is a class of DNA molecules that can perform catalytic functions with high selectivity towards specific metal ions. Due to its potential applications for biosensors and medical therapeutics, DNAzyme has been extensively studied to characterize the relationships between its biochemical properties and functions. Similar to protein enzymes and ribozymes, DNAzymes have been found to undergo conformational changes in a metal–ion–dependent manner for catalysis. Despite the important role the conformation plays in the catalysis process, such structural and dynamic information might not be revealed by conventional approaches. Here, by using the single–molecule fluorescence resonance energy transfer (smFRET) technique, we were able to investigate the detailed conformational dynamics of a uranyl–specific DNAzyme 39E. We observed conformation switches of 39E to a folded state with the addition of Mg<sup>2+</sup> and to an extended state with the addition of UO<sub>2</sub><sup>2+</sup>. Furthermore, 39E can switch to a more compact configuration with or without divalent metal ions. Our findings reveal that 39E can undergo conformational changes spontaneously between different configurations.https://www.mdpi.com/1422-0067/24/2/1212single–molecule fluorescence resonance energy transferDNAzymeconformational dynamicsmetal ions |
| spellingShingle | Yiming Zhang Zongzhou Ji Xin Wang Yi Cao Hai Pan Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics International Journal of Molecular Sciences single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions |
| title | Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics |
| title_full | Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics |
| title_fullStr | Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics |
| title_full_unstemmed | Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics |
| title_short | Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics |
| title_sort | single molecule study of dnazyme reveals its intrinsic conformational dynamics |
| topic | single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions |
| url | https://www.mdpi.com/1422-0067/24/2/1212 |
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