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Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
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Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
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Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
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53
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Dong Y, Mao Y. DNA Origami as Scaffolds for Self‐Assembly of Lipids and Proteins. Chembiochem 2019; 20:2422-2431. [DOI: 10.1002/cbic.201900073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/22/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteDepartment of MicrobiologyHarvard Medical School 450 Brookline Avenue Boston MA 02215 USA
- Intel Parallel Computing Center for Structural BiologyDana-Farber Cancer Institute 450 Brookline Avenue Boston MA 02215 USA
- Present address: CAS Key Laboratory of Colloid Interfaces and Chemical ThermodynamicsInstitute of ChemistryChinese Academy of Sciences No. 2 Zhongguancun Beiyijie Beijing 100190 P.R. China
| | - Youdong Mao
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteDepartment of MicrobiologyHarvard Medical School 450 Brookline Avenue Boston MA 02215 USA
- Intel Parallel Computing Center for Structural BiologyDana-Farber Cancer Institute 450 Brookline Avenue Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic PhysicsSchool of PhysicsCenter for Quantitative BiologyPeking University Beijing 100871 P.R. China
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Yang F, Cheng Y, Cao Y, Zhang Y, Dong H, Lu H, Zhang X. MicroRNA Triggered DNA “Nano Wheel” for Visualizing Intracellular microRNA via Localized DNA Cascade Reaction. Anal Chem 2019; 91:9828-9835. [DOI: 10.1021/acs.analchem.9b01487] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Fan Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Yaru Cheng
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Yu Cao
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Yiyi Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Haifeng Dong
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Huiting Lu
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
| | - Xueji Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, P.R. China
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Kizer M, Huntress ID, Walcott BD, Fraser K, Bystroff C, Wang X. Complex between a Multicrossover DNA Nanostructure, PX-DNA, and T7 Endonuclease I. Biochemistry 2019; 58:1332-1342. [PMID: 30794750 DOI: 10.1021/acs.biochem.9b00057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paranemic crossover DNA (PX-DNA) is a four-stranded multicrossover structure that has been implicated in recombination-independent recognition of homology. Although existing evidence has suggested that PX is the DNA motif in homologous pairing (HP), this conclusion remains ambiguous. Further investigation is needed but will require development of new tools. Here, we report characterization of the complex between PX-DNA and T7 endonuclease I (T7endoI), a junction-resolving protein that could serve as the prototype of an anti-PX ligand (a critical prerequisite for the future development of such tools). Specifically, nuclease-inactive T7endoI was produced and its ability to bind to PX-DNA was analyzed using a gel retardation assay. The molar ratio of PX to T7endoI was determined using gel electrophoresis and confirmed by the Hill equation. Hydroxyl radical footprinting of T7endoI on PX-DNA is used to verify the positive interaction between PX and T7endoI and to provide insight into the binding region. Cleavage of PX-DNA by wild-type T7endoI produces DNA fragments, which were used to identify the interacting sites on PX for T7endoI and led to a computational model of their interaction. Altogether, this study has identified a stable complex of PX-DNA and T7endoI and lays the foundation for engineering an anti-PX ligand, which can potentially assist in the study of molecular mechanisms for HP at an advanced level.
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Affiliation(s)
- Megan Kizer
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ian D Huntress
- Programs of Bioinformatics and Molecular Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Benjamin D Walcott
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Keith Fraser
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Christopher Bystroff
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Xing Wang
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
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