Cation‐Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride

Abstract

The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na and Mg concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl. These inverse behaviors are rationalized by a salting-out of Gdm to the hydrophobic DNA base stack. The effect of cation-induced DNA origami denaturation by GdmCl deserves consideration in the design of single-molecule studies and may potentially be exploited in future applications such as selective denaturation for purification purposes.

Structural stability of DNA origami nanostructures under application-specific conditions

“…(C)DNA origami triangles incubated at different temperatures in the presence of the chaotropic agent GdmCl at 6M concentration [ 61 ]. (D)DNA origami triangles in 4M GdmCl with varying MgCl 2 concentrations [ 62 ]. (E)DNA origami sheets without (left) and with (right) 8-MOP-based photo-cross-linking at 60 °C [ 63 ].…”

“…(D)is reproduced with permission from Ref. [ 62 ]; copyright John Wiley & Sons 2017. (E)is reproduced with permission from Ref.…”

“…1 C). Interestingly, DNAorigami stability at elevated temperatures can be improved in urea by increasing the concentration of cations in the buffer [ 62 ]. On the contrary, in GdmCl the elevated cation concentrations resulted in enhanced denaturation (see Fig.…”

“…On the contrary, in GdmCl the elevated cation concentrations resulted in enhanced denaturation (see Fig. 1 D), which was attributed to a salting-out of Gdm + ions to the hydrophobic base stack of the DNA origami [ 62 ]. These effects are expected to again show a superstructure-dependence, which, however, may turn out even more complex due to the interplay of stabilizing and destabilizing contributions involving both inter- and intramolecular electrostatic interactions.…”

“…DNA origami may maintain their structural integrity also under highly denaturing conditions in solution, for instance in the presence of highly concentrated chaotropic agents [ 61 ]. However, the interaction of such chaotropic denaturants with DNA origami nanostructures appears to be highly complex and exhibits some rather unexpected features, such as denaturant-specific modes of attack [ 61 ] and the gradual destabilization of DNA origami in GdmCl by increasing cation concentrations [ 62 ]. Understanding these complex processes will require further experimental and theoretical investigations of the molecular mechanisms involved.…”