Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant
Summary: An oxidative DNA-cleaving DNAzyme (PL) employs a double-cofactor model “X/Cu2+” for catalysis. Herein, we verified that reduced nicotinamide adenine dinucleotide (NADH), flavin mononucleotide, cysteine, dithiothreitol, catechol, resorcinol, hydroquinone, phloroglucinol, o-phenylenediamine,...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2020-10-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004220307471 |
| _version_ | 1819050972404514816 |
|---|---|
| author | Wenqian Yu Shijin Wang Dongling Cao Hongyue Rui Chengcheng Liu Yongjie Sheng Yanhong Sun Jin Zhang Jiacui Xu Dazhi Jiang |
| author_facet | Wenqian Yu Shijin Wang Dongling Cao Hongyue Rui Chengcheng Liu Yongjie Sheng Yanhong Sun Jin Zhang Jiacui Xu Dazhi Jiang |
| author_sort | Wenqian Yu |
| collection | DOAJ |
| description | Summary: An oxidative DNA-cleaving DNAzyme (PL) employs a double-cofactor model “X/Cu2+” for catalysis. Herein, we verified that reduced nicotinamide adenine dinucleotide (NADH), flavin mononucleotide, cysteine, dithiothreitol, catechol, resorcinol, hydroquinone, phloroglucinol, o-phenylenediamine, 3,3′,5,5'-tetramethylbenzidine, and hydroxylamine acted as cofactor X. According to their structural similarities or fluorescence property, we further confirmed that reduced nicotinamide adenine dinucleotide phosphate (NADPH), 2-mercaptoethanol, dopamine, chlorogenic acid, resveratrol, and 5-carboxyfluorescein also functioned as cofactor X. Superoxide anions might be the commonality behind these cofactors. We subsequently determined the conservative change of individual nucleotides in the catalytic core under four different cofactor X. The nucleotides A4 and C5 are highly conserved, whereas the conservative levels of other nucleotides are dependent on the types of cofactor X. Moreover, we observed that the minor change in the PL's secondary structure affects electrophoretic mobility. Finally, we characterized a highly efficient variant T3G and converted its double-cofactor NADH/Cu2+ to sole-cofactor NADH. |
| first_indexed | 2024-12-21T11:56:32Z |
| format | Article |
| id | doaj.art-92d7c1095d7d462dbc044d2688bb199c |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-21T11:56:32Z |
| publishDate | 2020-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-92d7c1095d7d462dbc044d2688bb199c2022-12-21T19:04:56ZengElsevieriScience2589-00422020-10-012310101555Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient VariantWenqian Yu0Shijin Wang1Dongling Cao2Hongyue Rui3Chengcheng Liu4Yongjie Sheng5Yanhong Sun6Jin Zhang7Jiacui Xu8Dazhi Jiang9Key Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, ChinaCollege of Animal Sciences, Jilin University, 5333# Xi'an Road, Changchun 130062, China; Corresponding authorKey Lab for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 2699# Qianjin Street, Changchun 130012, China; Corresponding authorSummary: An oxidative DNA-cleaving DNAzyme (PL) employs a double-cofactor model “X/Cu2+” for catalysis. Herein, we verified that reduced nicotinamide adenine dinucleotide (NADH), flavin mononucleotide, cysteine, dithiothreitol, catechol, resorcinol, hydroquinone, phloroglucinol, o-phenylenediamine, 3,3′,5,5'-tetramethylbenzidine, and hydroxylamine acted as cofactor X. According to their structural similarities or fluorescence property, we further confirmed that reduced nicotinamide adenine dinucleotide phosphate (NADPH), 2-mercaptoethanol, dopamine, chlorogenic acid, resveratrol, and 5-carboxyfluorescein also functioned as cofactor X. Superoxide anions might be the commonality behind these cofactors. We subsequently determined the conservative change of individual nucleotides in the catalytic core under four different cofactor X. The nucleotides A4 and C5 are highly conserved, whereas the conservative levels of other nucleotides are dependent on the types of cofactor X. Moreover, we observed that the minor change in the PL's secondary structure affects electrophoretic mobility. Finally, we characterized a highly efficient variant T3G and converted its double-cofactor NADH/Cu2+ to sole-cofactor NADH.http://www.sciencedirect.com/science/article/pii/S2589004220307471ChemistryBiochemistryBiocatalysis |
| spellingShingle | Wenqian Yu Shijin Wang Dongling Cao Hongyue Rui Chengcheng Liu Yongjie Sheng Yanhong Sun Jin Zhang Jiacui Xu Dazhi Jiang Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant iScience Chemistry Biochemistry Biocatalysis |
| title | Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant |
| title_full | Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant |
| title_fullStr | Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant |
| title_full_unstemmed | Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant |
| title_short | Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant |
| title_sort | insight into an oxidative dna cleaving dnazyme multiple cofactors the catalytic core map and a highly efficient variant |
| topic | Chemistry Biochemistry Biocatalysis |
| url | http://www.sciencedirect.com/science/article/pii/S2589004220307471 |
| work_keys_str_mv | AT wenqianyu insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT shijinwang insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT donglingcao insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT hongyuerui insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT chengchengliu insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT yongjiesheng insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT yanhongsun insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT jinzhang insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT jiacuixu insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant AT dazhijiang insightintoanoxidativednacleavingdnazymemultiplecofactorsthecatalyticcoremapandahighlyefficientvariant |