Colloidal Interactions and Self-Assembly Using DNA Hybridization

The specific binding of complementary DNA strands has been suggested as an ideal method for directing the controlled self-assembly of microscopic objects. We report the first direct measurements of such DNA-induced interactions between colloidal microspheres, as well as the first colloidal crystals assembled using them. The interactions measured with our optical tweezer method can be modeled in detail by well-known statistical physics and chemistry, boding well for their application to directed self-assembly. The microspheres' binding dynamics, however, have a surprising power-law scaling that can significantly slow annealing and crystallization.

Figure 1

(a) represents two microspheres trapped in the focal plane of a line optical tweezer. (b) shows microsphere surfaces chemically grafted with oligonucleotides, $s$, (sequence: $\underline{\mathrm{A}\mathrm{C}\mathrm{T}\mathrm{T}\mathrm{A}\mathrm{A}\mathrm{C}\mathrm{T}\mathrm{A}\mathrm{C}\mathrm{A}\mathrm{G}\mathrm{C}\mathrm{A}\mathrm{T}\mathrm{T}\mathrm{A}\mathrm{T}\mathrm{C}\mathrm{A}\mathrm{G}\mathrm{T}\mathrm{C}\mathrm{T}\mathrm{C}\mathrm{C}\mathrm{G}\mathrm{A}\mathrm{G}\mathrm{G}\mathrm{C}\mathrm{C}\mathrm{C}\mathrm{A}\mathrm{T}\mathrm{T}\mathrm{G}}\mathrm{\text{−}}\underline{\mathrm{A}\mathrm{T}\mathrm{T}\mathrm{C}\mathrm{A}\mathrm{C}\mathrm{A}\mathrm{C}\mathrm{A}\mathrm{C}\mathrm{G}\mathrm{T}}\mathrm{C}\mathrm{T}\mathbf{A}\mathbf{A}\mathbf{C}\mathbf{T}\mathbf{T}\mathbf{G}\mathbf{A}\mathbf{A}\mathbf{A}\mathbf{T}\mathbf{C}\mathbf{T}\mathbf{C}\mathbf{T}$). Linker oligonucleotides, $l$, (sequence: AGAGATTTCAAGTTCAGAGATTT-CAAGTT) can bridge between microspheres (shaded boxes) after hybridizing with the terminal 14 bases of $s$ (bold sequence). (c) same as (b) after hybridization of a third oligonucleotide complementary to $s$ (underlined sequence), forming a rigid rodlike spacer.

Figure 2

(a) Pair potential energy between two DNA-grafted microspheres as a function of separation, temperature, and spacer. The flexible spacer data, as in Fig. 1b, is at the top (circles). The rigid spacer data, as in Fig. 1c, is at the bottom (circles); it has a longer range and is stronger at a given temperature. Curves show our single parameter model, numerically blurred to account for instrumental resolution. Separation here is defined relative to the potential minimum. (b) shows the best fit values of hybridization free energy, $\Delta G_{\mathrm{h}\mathrm{y}\mathrm{b}}(T)$, for the flexible (○, $+$) and rigid (●, $\times$) spacers, with a priori prediction (line) with $2.5k_{B}T$ expected standard error (shaded region). (c) Bridge formation can be modeled as two coupled hybridization reactions: $s+l\leftrightarrow sl$ and $sl+s\leftrightarrow sls$. Approximate melting curves for these DNA structures are shown.

Figure 3

Optical micrographs of colloidal microspheres assembled by DNA hybridization. (a) Colloidal spheres with $\sim 14000\mathrm{D}\mathrm{N}\mathrm{A}/\mathrm{\text{sphere}}$ on a CML surface formed only fractal-like aggregates after 96 h. (b) Similar spheres with $\sim 3700\mathrm{D}\mathrm{N}\mathrm{A}/\mathrm{\text{sphere}}$ on a PEG surface formed crystallites, shown after 96 h of growth. (c) A close-up of the front surface of one of the crystallites. (d) All crystallites and aggregates melted immediately upon heating by $2°\mathrm{C}$, confirming they are held together by DNA bridges.

Figure 4

(a) shows the separation distance vs time for two DNA-grafted microspheres in a line optical tweezer, for 100 sec (top) and 10 sec (bottom and shaded box); flexible spacer, $T=43.0°\mathrm{C}$. The microspheres are alternately binding and unbinding, with a very broad distribution of bound lifetime. (b) and (c) show double logarithmic probability distributions of binding lifetime for the flexible and rigid spacer systems, respectively. The distributions have an anomalous power-law tail, with exponent roughly $-1.5$.