DNA origami is folded in salt-containing buffers, most commonly Mg2+. The cations are required to stabilize DNA duplexes, as DNA strands electrostatically repel each other in the absence of sufficient stabilizing ions. Usually MgCl2 is added between 5 and 20 mM, however the exact value depends on the structure. Variables affecting the optimal MgCl2 concentration include helical packing density, scaffold concentration, staple crossover routing, and more. For most origami, we recommend exploring synthesis yield at least within the 5–20 mM MgCl2 range.
For some applications, magnesium-free buffers may be required. For these applications researchers have two options. Structures can be folded using high concentrations of monovalent cations (like Na+ or K+) as a replacement1, or structures can be folded in magnesium buffers then buffer-switched into Mg-free buffers. To replace MgCl2, monovalent cations in the hundreds of millimolar concentration range are usually required. One advantage of removing MgCl2 from your buffer is that high concentrations of divalent cations can induce aggregation of origami2.
References
- Martin, T. G. & Dietz, H. Magnesium-free self-assembly of multi-layer DNA objects. Nat Commun 3, 1103 (2012).
- Ke, Y., Voigt, N. V., Gothelf, K. V. & Shih, W. M. Multilayer DNA Origami Packed on Hexagonal and Hybrid Lattices. J. Am. Chem. Soc. 134, 1770–1774 (2012).