Self-assembly of DNA nanostructures in different cations

Rodriguez, A.; Gandavadi, D.; Mathivanan, J.; Song, T.; Madhanagopal, B. R.; Talbot, H.; Sheng, J.; Wang, X.; Chandrasekaran, A. R.

doi:10.1101/2023.05.04.539416

bioRxiv · 10.1101/2023.05.04.539416

Self-assembly of DNA nanostructures in different cations

Rodriguez, A.·Gandavadi, D.·Mathivanan, J.·Song, T.·Madhanagopal, B. R.·Talbot, H.·Sheng, J.·Wang, X.·Chandrasekaran, A. R.

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Abstract

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg2+ and Na+). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif ([~]134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca2+, Ba2+, Na+, K+ and Li+ and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na+, K+ and Li+) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg2+, Ca2+ and Ba2+). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.

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Rodriguez, A., Gandavadi, D., Mathivanan, J., Song, T., Madhanagopal, B. R., Talbot, H., Sheng, J., Wang, X., Chandrasekaran, A. R.. 2023-05-04. Self-assembly of DNA nanostructures in different cations. https://doi.org/10.1101/2023.05.04.539416

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