The Formation and Displacement of Ordered DNA Triplexes in Self- Assembled Three-Dimensional DNA Crystals

Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnology. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addition of the Watson-Crick complement to a TFO containing a short toehold, and (c) the addition of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.

Automated summary

Reconfigurable DNA structures engineered through hybridization and self-assembly have potential applications in nanotechnology. This study demonstrates the creation of robust macroscopic DNA crystals through strand displacement of triplex-forming oligonucleotides (TFOs), which can be removed or replaced using different methods. X-ray diffraction analysis confirms the designed structure of the crystals in the presence of TFOs.