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...
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Autor*in:	Yiming Zhang [verfasserIn] Zongzhou Ji [verfasserIn] Xin Wang [verfasserIn] Yi Cao [verfasserIn] Hai Pan [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions

Übergeordnetes Werk:	In: International Journal of Molecular Sciences - MDPI AG, 2003, 24(2023), 2, p 1212
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:2, p 1212

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.3390/ijms24021212

Katalog-ID:	DOAJ081782535

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520			\|a 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.
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allfields	10.3390/ijms24021212 doi (DE-627)DOAJ081782535 (DE-599)DOAJ0a247c5a80304d4aaf334c51fd2feeb3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Yiming Zhang verfasserin aut Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions Biology (General) Chemistry Zongzhou Ji verfasserin aut Xin Wang verfasserin aut Yi Cao verfasserin aut Hai Pan verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 2, p 1212 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:2, p 1212 https://doi.org/10.3390/ijms24021212 kostenfrei https://doaj.org/article/0a247c5a80304d4aaf334c51fd2feeb3 kostenfrei https://www.mdpi.com/1422-0067/24/2/1212 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 2, p 1212
spelling	10.3390/ijms24021212 doi (DE-627)DOAJ081782535 (DE-599)DOAJ0a247c5a80304d4aaf334c51fd2feeb3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Yiming Zhang verfasserin aut Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions Biology (General) Chemistry Zongzhou Ji verfasserin aut Xin Wang verfasserin aut Yi Cao verfasserin aut Hai Pan verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 2, p 1212 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:2, p 1212 https://doi.org/10.3390/ijms24021212 kostenfrei https://doaj.org/article/0a247c5a80304d4aaf334c51fd2feeb3 kostenfrei https://www.mdpi.com/1422-0067/24/2/1212 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 2, p 1212
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allfieldsGer	10.3390/ijms24021212 doi (DE-627)DOAJ081782535 (DE-599)DOAJ0a247c5a80304d4aaf334c51fd2feeb3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Yiming Zhang verfasserin aut Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions Biology (General) Chemistry Zongzhou Ji verfasserin aut Xin Wang verfasserin aut Yi Cao verfasserin aut Hai Pan verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 2, p 1212 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:2, p 1212 https://doi.org/10.3390/ijms24021212 kostenfrei https://doaj.org/article/0a247c5a80304d4aaf334c51fd2feeb3 kostenfrei https://www.mdpi.com/1422-0067/24/2/1212 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 2, p 1212
allfieldsSound	10.3390/ijms24021212 doi (DE-627)DOAJ081782535 (DE-599)DOAJ0a247c5a80304d4aaf334c51fd2feeb3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Yiming Zhang verfasserin aut Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions Biology (General) Chemistry Zongzhou Ji verfasserin aut Xin Wang verfasserin aut Yi Cao verfasserin aut Hai Pan verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 24(2023), 2, p 1212 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:24 year:2023 number:2, p 1212 https://doi.org/10.3390/ijms24021212 kostenfrei https://doaj.org/article/0a247c5a80304d4aaf334c51fd2feeb3 kostenfrei https://www.mdpi.com/1422-0067/24/2/1212 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 2, p 1212
language	English
source	In International Journal of Molecular Sciences 24(2023), 2, p 1212 volume:24 year:2023 number:2, p 1212
sourceStr	In International Journal of Molecular Sciences 24(2023), 2, p 1212 volume:24 year:2023 number:2, p 1212
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topic_facet	single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions Biology (General) Chemistry
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container_title	International Journal of Molecular Sciences
authorswithroles_txt_mv	Yiming Zhang @@aut@@ Zongzhou Ji @@aut@@ Xin Wang @@aut@@ Yi Cao @@aut@@ Hai Pan @@aut@@
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callnumber-first	Q - Science
author	Yiming Zhang
spellingShingle	Yiming Zhang misc QH301-705.5 misc QD1-999 misc single–molecule fluorescence resonance energy transfer misc DNAzyme misc conformational dynamics misc metal ions misc Biology (General) misc Chemistry Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics
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topic_title	QH301-705.5 QD1-999 Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics single–molecule fluorescence resonance energy transfer DNAzyme conformational dynamics metal ions
topic	misc QH301-705.5 misc QD1-999 misc single–molecule fluorescence resonance energy transfer misc DNAzyme misc conformational dynamics misc metal ions misc Biology (General) misc Chemistry
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title	Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics
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title_sort	single–molecule study of dnazyme reveals its intrinsic conformational dynamics
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title_auth	Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics
url	https://doi.org/10.3390/ijms24021212 https://doaj.org/article/0a247c5a80304d4aaf334c51fd2feeb3 https://www.mdpi.com/1422-0067/24/2/1212 https://doaj.org/toc/1661-6596 https://doaj.org/toc/1422-0067
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