Reversible Binding of DNA on NiCl₂-Treated Mica by Varying the Ionic Strength

Abstract

The atomic force microscope is a key tool for investigating DNA conformation and DNA-protein interactions in liquid. The main advantage of this technique is that moving molecules can be studied in real time provided that molecules are sufficiently bound to the surface. Mg 2+ ions with a very low concentration of monovalent salt are generally used to attach DNA on mica because monovalent counterions inhibit the DNA electrostatic attraction with the surface. However, monovalent counterions at physiological concentrations are necessary to obtain specific DNA/protein interactions. To solve this problem, we propose a new protocol to obtain a reversible binding of DNA on NiCl 2-pretreated mica. This protocol uses Mg 2+ ions for monitoring DNA attachment on NiCl2-pretreated mica, which allows the DNA molecules to remain bound to the surface even at high NaCl concentration thanks to Ni 2+ ions adsorbed on the surface.

Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

“…Our surface diffusion protocol is based on biophysical studies, which demonstrated that changing the relative concentration of divalent and monovalent cations can profoundly change the surface mobility and reversibility of binding of long DNA on a mica surface 32,34,35 . To perform surface diffusion (Fig.…”

“…Calculation of the concentration of all ionic species for all buffers is explained in Supplementary Note 1 and summarized in Supplementary Table 1). Since monovalent cations are known to weaken the binding of DNA to mica 31,32,35,36 , we implemented the diffusion step by exchanging the buffer to one whose predominant cation is Na þ (B700 mM NaCl). During the diffusion step, we also mildly heated samples at a constant temperature (40°C, for B4 h; while heating above room temperature appears to facilitate the process, it is not essential for the surface diffusion of origami; evidence provided later).…”

“…During the diffusion step, we also mildly heated samples at a constant temperature (40°C, for B4 h; while heating above room temperature appears to facilitate the process, it is not essential for the surface diffusion of origami; evidence provided later). Since Ni 2 þ is known to bind DNA to mica more strongly than Mg 2 þ does 29,37 , even in the presence of competing Na þ ions 35 , we used it to implement the immobilization step. Adding concentrated Ni 2 þ solution (yielding B1 mM Ni 2 þ in the sample) stopped diffusion and 'froze' the product structures onto the surface.…”

“…Thus divalent cations, such as Mg 2 þ and Ni 2 þ , are often described as mediating the binding of DNA to mica by bridging the negative charges on the DNA backbone and those on the mica 29,31,35,36,39 . This is a great simplification of divalent-cation-mediated DNA-mica binding, since the strength of binding for a particular cation concentration depends strongly on the identity of the cation, the size and geometry of the DNA object in question and the method of sample preparation.…”

“…Further complicating matters, monovalent cations commonly present in buffer solutions such as Na þ , K þ or TrisH þ can decrease the interaction of divalent cations with DNA and mica. 31,32,35,36 For particular cations, for linear dsDNA, three studies by the same group have been successful in explaining strong-to-weak binding transitions of particular relevance to our system 31,32,40 .…”