Single-stranded templates as railroad tracks for hierarchical assembly of DNA origami

Abstract

DNA origami is one of the most effective tools for bottom-up construction of novel objects and devices at the nanometer-scale. However, many applications require larger structures than can be obtained with the conventional single-stranded scaffold, typically 7249 nucleotides. Here, we address this limitation by developing custom-made single-stranded scaffolds that bind pre-assembled origami tiles and induce their one-dimensional organization in high yields. Our synthetic method allows the conversion of multiple repetitive and unique sequences into correctly assembled, large backbones, and to finely tune the position and frequency of each building block. Granted with these regions, three and five origami tiles were successfully arranged in 1-D with the aid of one or two scaffolds, forming a nano-"railroad track". This new method increases length scale in DNA origami without increasing cost and complexity, and is anticipated to increase the yield of other approaches aiming to assemble large origami structures.

Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies

“…Streptavidin–biotin magnetic bead separation was used to isolate the ssDNA product similar to the previously described method in this review. Scaffolds produced by sequential growth were used to fold DNA nanotubes, which served as the template for 15 nm streptavidin-coated quantum dots [ 102 ], as well as to create ‘railroad tracks’ to join DNA origami plates for the organization of higher-order structure assembly [ 114 ]. This scaffold synthesis method offers the ability to produce a scaffold with an arbitrary sequence, whereas other methods are limited to existing biological templates and/or the incorporation of enzyme-specific recognition sites.…”

DNA nanotechnology-based nucleic acid delivery systems for bioimaging and disease treatment

“…To address this issue, long double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) has been applied to construct two-dimensional DNA origami instead of conventional DNA scaffolds. [44][45][46][47] For instance, Sleiman et al exploited a sequential growth method for synthesizing longer repetitive ssDNA scaffolds that can be prepared using standard polymerase chain reaction (PCR) and easily modified, resulting in large DNA origami surfaces with high yields. 46 Li's group assembled different dsDNA fragments and the M13 replication origin into a circular recombinant phage and transformed it into E. coli cells, producing long circular ssDNA scaffolds with customized sequences and lengths for the self-assembly of various nanostructures, such as rectangular and triangular DNA origamis (Fig.…”

Recent Advances of DNA Origami Technology and Its Application in Nanomaterial Preparation

“…Sleiman et al obtained size‐expanded DNA nanoribbons by using the scaffold which was amplified by PCR to assemble rectangular DNA origami. [ 15 ] 2) The second way to expand the size of the assemblies was extending the length of DNA scaffold. Yan's group [12b] successfully constructed triangular DNA origami with enlarged size by denaturing dsDNA into ssDNA at high temperature to extend the length of the scaffold.…”