DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails

Abstract

The DNA origami method allows the folding of long, single-stranded DNA sequences into arbitrary two-dimensional structures by a set of designed oligonucleotides. The method has revealed an unexpected strength and efficiency for programmed self-assembly of molecular nanostructures and makes it possible to produce fully addressable nanostructures with wide-reaching application potential within the emerging area of nanoscience. Here we present a user-friendly software package for designing DNA origami structures ( http://www.cdna.dk/origami ) and demonstrate its use by the design of a dolphin-like DNA origami structure that was imaged by high-resolution AFM in liquid. The software package provides automatic generation of DNA origami structures, manual editing, interactive overviews, atomic models, tracks the design history, and has a fully extendable toolbox. From the AFM images, it was demonstrated that different designs of the dolphin tail region provided various levels of flexibility in a predictable fashion. Finally, we show that the addition of specific attachment sites promotes dimerization between two independently self-assembled dolphin structures, and that these interactions stabilize the flexible tail.

Self-assembly of a nanoscale DNA box with a controllable lid

“…Furthermore, we have demonstrated dynamic control and programmability of the box lid. In an earlier study, we demonstrated that DNA origami structures can be designed that have tunable flexible properties 16 , and here we further show that dynamic changes can be induced by sensing external signals in the environment. The application of such a 'nanorobotic' device could be to restrict the transport of material in or out of the box in a controlled fashion.…”

“…The software package used for the box design consists of a sequence editor and an extendable algorithm toolbox 16 . We developed a program for creating realistic 3D models, which facilitated the design of the 3D edge-to-edge staple strand crossovers.…”

“…We prepared the m13mp18 DNA as described previously 16 . The assembly reactions were performed in Tris-acetate-EDTA buffer with 12.5 mM MgAc (TAEM), 1.6 nM M13 and fivefold excess of each oligonucleotide.…”

“…We designed the DNA box by using a recently developed software package 16 to fold six DNA origami sheets along the circular, singlestranded DNA genome of the M13 bacteriophage (faces indicated with the letters A-F, Fig. 1a).…”

Engineered RNA Nanodesigns for Applications in RNA Nanotechnology

“…The use of these rules has resulted in the engineering and characterization of numerous DNA 3D nanoscaffolds with different connectiviities [7][8][9][10][11][12][13][14][15][16][17][18] and the ability for some of them to promote targeted delivery by functioning as DNA nano-capsules [19][20][21] or DNA nano-carriers for other functionialities [22]. Another powerful technique called DNA "origami", developed by Paul Rothemund [23], has been extended from its original scope for designing different 2D DNA shapes [24] and functional templates [25][26][27][28] Abstract Nucleic acids have emerged as an extremely promising platform for nanotechnological applications because of their unique biochemical properties and functions. RNA, in particular, is characterized by relatively high thermal stability, diverse structural flexibility, and its capacity to perform a variety of functions in nature.…”