3D DNA origami designed with caDNAno

Abstract

For about three decades, DNA-based nanotechnology has been undergoing development as an assembly method for nanostructured materials. The DNA origami method pioneered by Rothemund paved the way for the formation of 3D structures using DNA self assembly. The origami approach uses a long scaffold strand as the input for the self assembly of a few hundred staple strands into desired shapes. Herein, we present a 3D origami "roller" (75 nm in length) designed using caDNAno software. This has the potential to be used as a template to assemble nanoparticles into different pre-defined shapes. The "roller" was characterized with agarose gel electrophoresis, atomic force microscopy (AFM) and transmission electron microscopy (TEM). DNA nanotechnology uses the molecular recognition properties of DNA to create artificial DNA structures for specific technological purposes. This branch of nanotechnology holds great promise for a vast range of applications in fields such as medicine, materials science, biology and biochemistry. The theoretical framework for using DNA as a building material for the construction of nanoscale devices was laid down by Seeman [1,2]. This is made possible due to DNA's capacity for programmable self-assembly and its high stability. In subsequent works, several authors have used DNA to construct an increasing number of composite structures [3][4][5][6][7][8][9]. After the potential of DNA self-assembly was well established, Rothemund [10] introduced the method of DNA origami which is versatile in constructing pre-defined designs. The process involves heating a mixture of scaffold and staple strands to several degrees Celsius and annealing at room temperature for several hours to yield single-layered structures. For multilayered structures, several days are needed for folding [11,12]. This simple, "one-pot" method uses several hundred staple strands to direct the folding of a long, single scaffold strand of DNA into pre-defined shapes [10]. Applications have emerged based on DNA origami, such as using it to arrange metal nanoparticles [13][14][15], to design and construct detergent-resistant liquid crystal DNA-nanotubes that can in turn be used to induce weak alignment of membrane proteins [16], to produce label-free RNA hybridization probes [17], and for the self-assembly of carbon nanotubes into two-dimensional geometries [18].Here, we describe the design of a 3D origami structure, which resembles a roller, using the open source software package, caDNAno, constrained to the honeycomb framework [12]. We analyze and characterize the structure obtained using gel electrophoresis, atomic force microscopy (AFM) and transmission electron microscopy (TEM). Our "roller" design has the potential to be used to arrange nanoparticles into a range of different shapes.

Measuring the Conformation and Persistence Length of Single-Stranded DNA Using a DNA Origami Structure

“…The DNA origami structure was designed using caDNAno. , Because of the “parity problem” (the two strands emerging from each rod should exit from its two opposite ends), each rod was designed to consist of an odd number of seven dsDNA and to fold at a specific site of the plasmid (Supporting Information Note 3).…”

Dna Origami Site-Specific Arrangement of Gold Nanoparticles

“…25 The structure was designed by caDNAno 5 software using single stranded M13mp18 DNA (7249 nt, New England Biolab.) as the sca®old and the 201 generated staples.…”

“…25 We used the 48-helix bundle multilayer in the middle of the roller structure to assemble the gold nanoparticles after making the following modi¯cations to the staple strands at our designed binding sites: We designed di®erent DNA sticky ends at speci¯c locations (see Fig. 2) on the surface of the multilayer by extending the sequence from selected staple strands of the roller template.…”

“…Our structure has been characterized and described. 25 We determined the speci¯c positions on the outside tube where gold nanoparticles were to be attached from the caDNAno software. We then designed these attachment sites by extending speci¯c staples with sticky ends that will hybridize with complementary sticky ends conjugated to the gold nanoparticles by thiol chemistry.…”

DNA Origami as a Tool to Design Asymmetric Gold Nanostructures

“…For single-layered origami structures the mixture is heated for a few hours to fold while multi-layered structures can take up to days. The DNA origami method can produce both 2-D and 3-D structures of pre-arranged shapes (Rothemund, 2006;Douglas et al, 2009a;Douglas et al, 2009b;Amoako et al, 2013). The approximately 7200 base-scaffold and the numerous staples are mixed together in a suitable buffer during folding and then annealed over a certain temperature range (Rothemund, 2006;Douglas et al, 2009b;Castro et al, 2011).…”