Structure of Nanoscale Truncated Octahedral DNA Cages: Variation of Single-Stranded Linker Regions and Influence on Assembly Yields

Abstract

The assembly, structure, and stability of DNA nanocages with the shape of truncated octahedra have been studied. The cages are composed of 12 double-stranded B-DNA helices interrupted by single-stranded linkers of thymidines of varying length that constitute the truncated corners of the structure. The structures assemble with a high efficiency in a one-step procedure, compared to previously published structures of similar complexity. The structures of the cages were determined by small-angle X-ray scattering. With increasing linker length, there is a systematic increase of the cage size and decrease of the twist angle of the double helices with respect to the symmetry planes of the cage structure. In the present study, we demonstrate the length of the single-stranded linker regions, which impose a certain degree of flexibility to the structure, to be the important determinant for efficient assembly. The linker length can be decreased to three thymidines without affecting assembly yield or the overall structural characteristics of the DNA cages. A linker length of two thymidines represents a sharp cutoff abolishing cage assembly. This is supported by energy minimization calculations suggesting substantial hydrogen bond deformation in a cage with linkers of two thymidines.

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

“…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.…”

“…This was accomplished by a modification to our previously published DNA cage design. 20,21 In this structure eight oligonucleotides of equal length hybridize to form a truncated octahedron. According to SAXS analysis 20,21 the inner cavity of the presented design has a diameter of approximately 10À12 nm, which is large enough to accommodate the dimensions of HRP.…”

Calculation of Small-Angle Scattering Patterns

“…Oliveira and collaborators [45,46] used this kind of procedure to show the first analysis of nanocage structures using scattering radiation techniques. The authors were interested in discovering the influence in the stability and yield to build experimental DNA octahedron nanocages in solutions, using double and single DNA strands [45].…”

“…The authors were interested in discovering the influence in the stability and yield to build experimental DNA octahedron nanocages in solutions, using double and single DNA strands [45]. Then, to perform the modeling and compare with experimental data, the double DNA helix models are positioned in the edge, in octahedron geometry, that was truncated by single DNA strands that perform linkers between the helices.…”

A New Euler's Formula for DNA Polyhedra

“…Since the synthesis of the DNA cube [6], a rich variety of DNA polyhedra, including tetrahedron [7], octahedron [8], dodecahedron [9], icosahedrons [10], and buckyball [11] have now been reported in the literature. In these nano-constructions, each face is made of closed, interlocked DNA rings, each edge is made of double-helix [12] or quadruplex-helix [13]–[15] DNA strands, and each vertex represents an immobile multi-arm junction. The interest in these species is rapidly increasing not only for their potential properties but also for their intriguing architectures and topologies.…”