Abstract
DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers.
Highlights
DNA is a powerful tool that can be used to create nanosized architectures and devices because of its synthetic accessibility and ability to self-assemble (1–6)
Various types of DNA–rigid-molecule conjugates have been reported (12–17). In these cases, the rigid linker is connected to the flexible phosphodiester backbone of the DNA oligomer
In our DNA unit design, each terminal of the rigid molecule, which is composed of phenylene and ethynylene groups, is joined through a triple bond at the 5 -position of the uridine base located in the middle of the DNA duplexes (Figure 1B)
Summary
DNA is a powerful tool that can be used to create nanosized architectures and devices because of its synthetic accessibility and ability to self-assemble (1–6). For assembling the hexagonal DNA origami, two hexagonal origami monomers, Hex 1 and Hex 2 (5 nM), with four connection strands at the D- and A-edges, respectively, were annealed with H-shaped DNA (H4 linker, 6–8 equiv) from 40 to 15◦ C at a rate of −1.0◦ C/min. (2) After the first elongation, the support was removed from the synthesizer, and a coupling reaction between two reactive alkynes (an oligonucleotide on the support and a modified monomeric nucleotide in solution) was performed by using a solid-phase Glaser reaction (Scheme 1, step A).
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