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Andersen FF, Knudsen B, Oliveira CLP, Frøhlich RF, Krüger D, Bungert J, Agbandje-McKenna M, McKenna R, Juul S, Veigaard C, Koch J, Rubinstein JL, Guldbrandtsen B, Hede MS, Karlsson G, Andersen AH, Pedersen JS, Knudsen BR. Assembly and structural analysis of a covalently closed nano-scale DNA cage. Nucleic Acids Res 2008; 36:1113-9. [PMID: 18096620 PMCID: PMC2275108 DOI: 10.1093/nar/gkm1124] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 11/29/2007] [Accepted: 12/03/2007] [Indexed: 11/12/2022] Open
Abstract
The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA-interacting enzymes. More recently, strategies for synthesis of more complex two-dimensional (2D) and 3D DNA structures have emerged. However, the building of such structures is still in progress and more experiences from different research groups and different fields of expertise are necessary before complex DNA structures can be routinely designed for the use in basal science and/or biotechnology. Here we present the design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron, as defined by the double-stranded DNA helices that assembles from eight oligonucleotides with a yield of approximately 30%. As demonstrated by Small Angle X-ray Scattering and cryo-Transmission Electron Microscopy analyses the eight-stranded DNA structure has a central cavity larger than the apertures in the surrounding DNA lattice and can be described as a nano-scale DNA cage, Hence, in theory it could hold proteins or other bio-molecules to enable their investigation in certain harmful environments or even allow their organization into higher order structures.
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Affiliation(s)
- Felicie F. Andersen
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Bjarne Knudsen
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Cristiano Luis Pinto Oliveira
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Rikke F. Frøhlich
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Dinna Krüger
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Jörg Bungert
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Mavis Agbandje-McKenna
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Robert McKenna
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Sissel Juul
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Christopher Veigaard
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Jørn Koch
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - John L. Rubinstein
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Marianne S. Hede
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Göran Karlsson
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Anni H. Andersen
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Jan Skov Pedersen
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
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