Microscopics of Complexation between Long DNA Molecules and Positively Charged Colloids

Extensive atomic force and electron microscopy reveal a new, generic DNA-colloid complex with a fixed number of DNA bases per colloid. The fiber shaped complex is stable in the presence of excess colloids in the solution. As more DNA is added to the solution and the ratio between colloids and DNA approaches the fiber’s stoichiometry, the system undergoes a sharp coagulation transition. The system is restabilized at even higher DNA concentrations through localization of small colloid clusters on extensive DNA networks.

Figure 1

Phase diagram of colloid-$\lambda$-DNA complexation as a function of DNA and colloid quantities in $800\mu \mathrm{l}$. Phase boundaries are determined both by linear extrapolation of the reaction rate in phase II (e.g., inset) averaged over the first 6 min to zero reaction rate (solid symbols) and by sedimentation after $\sim 14\mathrm{h}$ (open symbols). For a given colloid concentration, the DNA concentration for which the reaction rate is maximal (see inset) is shown by solid circles and the generic cluster stoichiometry is plotted by a dashed line. Diamonds depict the concentrations corresponding to the graphs in Fig. 3. Inset: peak OD reduction rate, $[d(\mathrm{O}\mathrm{D})/dt]/\mathrm{O}\mathrm{D}$ (averaged over the first 6 min), as a function of DNA concentration for different numbers of colloids in $800\mu \mathrm{l}$ solution. The microscopic content of the three phases is plotted schematically. Phase I consists of generic nucleocolloid fibers in coexistence with free colloids. Phase II comprises large nucleocolloid clusters with some bare DNA segments and molecules. Phase III comprises small colloidal clusters localized on extensive DNA networks.

Figure 2

(a) SEM image of a sample in phase I revealing small clusters in coexistence with free colloids. (b) SEM image of a sample in phase II revealing large, typically elongated clusters (thousands of colloids) and no free colloids. (c) AFM image of a sample in phase III revealing small clusters (up to tens of colloids) localized on DNA networks. (d) TEM image of an extended cluster in phase I. The dashed line serves as a guide to the eye.

Figure 3

Cluster size distributions obtained from SEM images for different amounts of $\lambda$-DNA and $\approx 6.04\times {10}^{11}$ colloids in $800\mu \mathrm{l}$ after 1 h reaction time. Distributions are normalized so that the total number of colloids is equal between samples. The table gives the percent of free colloids, colloids in generic clusters (clusters $<35$), and colloids in larger clusters, for different amounts of DNA in $800\mu \mathrm{l}$ solution.

Figure 4

Main panel: cluster size distribution of bound colloids for DNA molecules of different length at $0.7\mu \mathrm{g}$ DNA and $\approx 6.04\times {10}^{11}$ colloids in $800\mu \mathrm{l}$ solution. The free colloid distribution has been subtracted and the distributions are normalized to unity. Inset: (left axis) percent of free colloids as a function of DNA concentration (circles: $\lambda$-DNA; square: Hind III restriction fragment); (right axis) percent of clusters larger than 35 colloids as a function of DNA concentration for $\lambda$-DNA (squares). Colloid concentration in all samples, $\approx 6.04\times {10}^{11}$ in $800\mu \mathrm{l}$ solution. The amount of free colloids is determined by fitting the measured cluster size distribution to the free colloid distribution at clusters $<6$. The fraction of free colloids is taken to be the ratio between the number of colloids contained in the free colloid fit and the total number of colloids measured in the sample.