Anionic Polyelectrolyte Adsorption on Mica Mediated by Multivalent Cations: A Solution to DNA Imaging by Atomic Force Microscopy under High Ionic Strengths

Abstract

Adsorption of DNA molecules on mica, a highly negatively charged surface, mediated by divalent or trivalent cations is considered. By analyzing atomic force microscope (AFM) images of DNA molecules adsorbed on mica, phase diagrams of DNA molecules interacting with a mica surface are established in terms of concentrations of monovalent salt (NaCl) and divalent (MgCl2) or multivalent (spermidine, cobalt hexamine) salts. These diagrams show two transitions between nonadsorption and adsorption. The first one arises when the concentration of multivalent counterions is larger than a limit value, which is not sensitive to the monovalent salt concentration. The second transition is due to the binding competition between monovalent and multivalent counterions. In addition, we develop a model of polyelectrolyte adsorption on like-charged surfaces with multivalent counterions. This model shows that the correlations of the multivalent counterions at the interface between DNA and mica play a critical role. Furthermore, it appears that DNA adsorption takes place when the energy gain in counterion correlations overcomes an energy barrier. This barrier is induced by the entropy loss in confining DNA in a thin adsorbed layer, the entropy loss in the interpenetration of the clouds of mica and DNA counterions, and the electrostatic repulsion between DNA and mica. The analysis of the experimental results provides an estimation of this energy barrier. We then discuss some important issues, including DNA adsorption under physiological conditions.

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

“…Notably, the bulk concentration of Mg 2 þ is found to be the worst predictor of lattice formation. The onset of lattice formation behaves similar to a previously observedñ s2 -determined strong-to-weak binding transition for circular dsDNA 32 , and may indicate an analogous transition for DNA origami on mica, one which enables surface diffusion. However the high strength of origami binding yields a transition at a lowerñ s2 value (B0.2 rather than B0.65), and good lattice formation appears to require more than just surface diffusion sinceñ s2 o0:04 decreases lattice incorporation rates.…”

“…For example, a daily experience in our lab is that 12.5 mM Mg 2 þ is insufficient to provide stable buffer imaging of 14.5 kilonucleotide (knt) linear dsDNA that often occurs as a minor impurity of m13 dsDNA in origami preparations. Similar experience with dsDNA in many labs has led to the idea that Mg 2 þ binds DNA to mica but only very weakly 29,32 . However, 12.5 mM Mg 2 þ provides for stable buffer imaging of 14.5 knt single-layer DNA origami such as rectangles or triangles, but not for structures which present areas significantly smaller than the 7,000 nm 2 area of a 14.5 knt single- layer origami, such as a B5 knt single-layer rectangle 1 .…”

“…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).…”

“…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.…”