Adsorption of DNA to Mica Mediated by Divalent Counterions: A Theoretical and Experimental Study

Abstract

The adsorption of DNA molecules onto a flat mica surface is a necessary step to perform atomic force microscopy studies of DNA conformation and observe DNA-protein interactions in physiological environment. However, the phenomenon that pulls DNA molecules onto the surface is still not understood. This is a crucial issue because the DNA/surface interactions could affect the DNA biological functions. In this paper we develop a model that can explain the mechanism of the DNA adsorption onto mica. This model suggests that DNA attraction is due to the sharing of the DNA and mica counterions. The correlations between divalent counterions on both the negatively charged DNA and the mica surface can generate a net attraction force whereas the correlations between monovalent counterions are ineffective in the DNA attraction. DNA binding is then dependent on the fractional surface densities of the divalent and monovalent cations, which can compete for the mica surface and DNA neutralizations. In addition, the attraction can be enhanced when the mica has been pretreated by transition metal cations (Ni(2+), Zn(2+)). Mica pretreatment simultaneously enhances the DNA attraction and reduces the repulsive contribution due to the electrical double-layer force. We also perform end-to-end distance measurement of DNA chains to study the binding strength. The DNA binding strength appears to be constant for a fixed fractional surface density of the divalent cations at low ionic strength (I < 0.1 M) as predicted by the model. However, at higher ionic strength, the binding is weakened by the screening effect of the ions. Then, some equations were derived to describe the binding of a polyelectrolyte onto a charged surface. The electrostatic attraction due to the sharing of counterions is particularly effective if the polyelectrolyte and the surface have nearly the same surface charge density. This characteristic of the attraction force can explain the success of mica for performing single DNA molecule observation by AFM. In addition, we explain how a reversible binding of the DNA molecules can be obtained with a pretreated mica surface.

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

“…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).…”

“…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.…”

“…Ni 2 þ apparently binds to mica so strongly that Ni 2 þ pretreatment of the surface is all that is necessary to immobilize short dsDNA 31,40 . The idiosyncratic properties of each divalent metal cation with respect to DNA binding to mica have been partially attributed to cationic radius or enthalpies of hydration 29 or specific complexation of the ions with DNA or mica 31 , but no theory consistently explaining the behaviour of all divalent cations seems to exist. 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.…”

“…For artificial DNA nanostructures, cation-dependent mica binding has not been studied quantitatively. In particular, the competition between monovalent and divalent cations measured in biophysical studies 31,32 has not been considered, perhaps because it has been assumed that divalent cations dominate the DNA-mica interaction.…”

Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level

“…Also, while DNA hybridization near a mica surface has not been widely studied, it is reasonable to expect that there could be significant differences from hybridization in solution: at the very least, the "salt bridge" of divalent cations (in our case, Mg 2+ ) between the DNA and mica would result in a very different and likely nonhomogenous ionic environment. 21 …”