Self‐Assembly of DNA Nanostructures in Different Cations

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 that restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions are 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.

Mechanism of DNA origami folding elucidated by mesoscopic simulations

“…Atomic force microscopy (AFM) is typically used for direct imaging and is able to resolve individual origami species, providing insight into the folded character of structures 19 – 23 . Using this approach, researchers have shown that the folded product of DNA origami can be significantly influenced by design and fabrication conditions such as staple sequences 24 , ionic conditions 25 , and staple-scaffold stoichiometry 26 . While useful, AFM can provide only limited information because it has relatively low temporal resolution.…”

Design and Assembly of a Cargo-agnostic Hollow Two-lidded DNA Origami Box for Drug Delivery

“…Previous studies have reported that assembly in other salts results in enhanced DNA origami stability. 35,36 We probed whether these hollow DNA boxes can be assembled in sodium chloride in the absence of magnesium salts. No dramatic changes were observed when the hollow DNA origami boxes were assembled in sodium chloride ( Supplemental Figure 5C and Figure 4D ).…”

“…This may suggest that the hollow DNA origami boxes are either transiently coated by serum components or transiently aggregate. 22,35,37,38 In contrast, other groups have shown that simpler DNA origami structures are considered to be completely dissembled after 24 h in the presence of 10-20% FBS. 22,35,37 However, complete disassembly would not explain the DNA origami box shift back to its original band location after three days.…”

“…22,35,37,38 In contrast, other groups have shown that simpler DNA origami structures are considered to be completely dissembled after 24 h in the presence of 10-20% FBS. 22,35,37 However, complete disassembly would not explain the DNA origami box shift back to its original band location after three days. As with the other conditions, the hollow DNA origami boxes showed robust stability in serum and displayed no smearing or changes in band intensity.…”

DNA nanostructure decoration: a how-to tutorial

“…An in-plane angle of π/3 rad (60°) is a commonly accepted value in biological contexts [58,59]. This angle is likely to be lower in DNA nanostructures, and may vary between designs, particularly for 2D and 3D structures, and quantification of these angles in origami or other DNA nanostructures has been a subject of few publications, typically in the context of mechanical properties [60], ion dependent reconfiguration [61,62], novel characterization [63][64][65], and bistable physical isomorphs [66,67]. It is worth noting that both the schematics in figure 12, and in most CAD tools, can visually imply larger spacings than occur practically.…”