Nucleic Acids Research Advance Access originally published online on December 20, 2007
Nucleic Acids Research 2008 36(4):1113-1119; doi:10.1093/nar/gkm1124
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Nucleic Acids Research, 2008, Vol. 36, No. 4 1113-1119
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Assembly and structural analysis of a covalently closed nano-scale DNA cage
1Department of Molecular Biology and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, C.F. Møllers Allé, Bldg. 1130, 8000 Aarhus C, Denmark, 2CLC bio A/S, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark, 3Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, 8000 Aarhus C, Denmark, 4Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, P.O. Box 100245, 1600 SW Archer Road, Gainesville, FL 32610, USA, 5Department of Pathology, Aarhus Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark, 6Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8, 7Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Blichers Allé, Postbox 50, 8830 Tjele, Denmark and 8Department of Physical and Analytical Chemistry, Division of Physical Chemistry, Uppsala University, Box 579, 751 23 Uppsala, Sweden
*To whom correspondence should be addressed. Tel: +45 8942 2703; Fax: +45 8942 2612; Email: brk{at}mb.au.dk
Received September 21, 2007. Revised November 29, 2007. Accepted December 3, 2007.
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 
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.