Assembly and structural analysis of a covalently closed nano-scale DNA cage

Andersen, Félicie F.; Knudsen, Bjarne; Oliveira, Cristiano L. P.; Frøhlich, Rikke; Krüger, Dinna; Bungert, Jörg; Agbandje‐McKenna, Mavis; McKenna, Robert; Juul, Sissel; Veigaard, Christopher; Koch, Jørn; Rubinstein, John L.; Guldbrandtsen, Bernt; Hede, Marianne Smedegaard; Karlsson, Göran; Andersen, Anders H.; Pedersen, Jan Skov; Knudsen, Birgitta R.

doi:10.1093/nar/gkm1124

Cited by 109 publications

(136 citation statements)

References 33 publications

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“…By quantification of the band representing fully assembled Cage hp (3T) relative to the higher and lower-mobility products the yield of the correctly assembled Cage hp (3T) was estimated to approximately 30À40%, which is comparable to the yield previously reported for Cage(3T)À Cage(7T). 20,21 The anticipated yield of a DNA nanostructure was previously demonstrated to correlate to the number of double-stranded helices in the structure with a decrease in yield as the number of duplexes increase. 44 Factors hampering yield are slight variations in DNA strand concentrations and potential topological 3T and OL2hp 3T ; OL1hp 3T ÀOL3hp 3T ; OL1hp 3T ÀOL4hp 3T ; OL1hp 3T ÀOL4hp 3T and OL5 3T ; OL1hp 3T ÀOL4hp 3T and OL5 3T ÀOL6 3T ; OL1hp 3T À OL4hp 3T and OL5 3T ÀOL7 3T ; OL1hp 3T ÀOL4hp 3T and OL5 3T ÀOL8 3T to analysis in a native polyacrylamide gel.…”

Section: Resultsmentioning

confidence: 99%

Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage

et al. 2013

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We demonstrate temperature-controlled encapsulation and release of the enzyme horseradish peroxidase using a preassembled and covalently closed three-dimensional DNA cage structure as a controllable encapsulation device. The utilized cage structure was covalently closed and composed of 12 double-stranded B-DNA helices that constituted the edges of the structure. The double stranded helices were interrupted by short single-stranded thymidine linkers constituting the cage corners except for one, which was composed by four 32 nucleotide long stretches of DNA with a sequence that allowed them to fold into hairpin structures. As demonstrated by gel-electrophoretic and fluorophore-quenching experiments this design imposed a temperature-controlled conformational transition capability to the structure, which allowed entrance or release of an enzyme cargo at 37 °C while ensuring retainment of the cargo in the central cavity of the cage at 4 °C. The entrapped enzyme was catalytically active inside the DNA cage and was able to convert substrate molecules penetrating the apertures in the DNA lattice that surrounded the central cavity of the cage.

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Section: Resultsmentioning

confidence: 99%

Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage

et al. 2013

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“…In particular, this means that in oxDNA, the AA and TT stacking interactions are the same, whereas it is well known that the AA stacking interaction is significantly stronger than the TT interaction, an important property for DNA nanotechnology, for example, where poly-T single-stranded regions are often used as flexible linkers. 61,62 To remedy this, we use new experimental data to reparameterise the AA and TT stacking interactions in the model.…”

Section: Introductionmentioning

confidence: 99%

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Snodin

Randisi

Mosayebi

et al. 2015

The Journal of Chemical Physics

317

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We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single-and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na + ] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA. C 2015 AIP Publishing LLC. [http://dx

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“…Several assembly strategies have been developed for building complex threedimensional (3D) DNA nanostructures [2][3][4][5][6][7][8] . Recently, the DNA 'origami' method was used to build two-dimensional addressable DNA structures of arbitrary shape 9 that can be used as platforms to arrange nanomaterials with high precision and specificity [9][10][11][12][13] .…”

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confidence: 99%