Electrostatically Driven Interactions between Hybrid DNA-Carbon Nanotubes

Single-stranded DNA is able to wrap around single-wall carbon nanotubes (CNT) and form stable DNA-CNT hybrids that are highly soluble in solution. Here we report quantitative measurements and analysis of the interactions between DNA-CNT hybrids at low salts. Condensation of DNA-CNT hybrids by neutral osmolytes leads to liquid crystalline phases, and varying the osmotic pressure modulates the interhybrid distance that is determined by x-ray diffraction. Thus obtained force-distance dependencies of DNA-CNT hybrids show a remarkable resemblance to that of double-stranded DNA with differences that can be largely accounted for by their different diameters. This establishes their common physical nature of electrostatically driven interactions. Quantitative modeling further reveals the roles of hydration in mediating the interhybrid forces within the last nanometer of surface separation. This study also suggests the utility of osmotic pressure to control DNA-CNT assemblies at subnanometer precision.

Figure 1

Osmolyte-driven self-assembly of DNA-CNT hybrids and structure characterization. (a) One proposed DNA-CNT structure, the $\beta$-barrel DNA helical motif around a (6, 5) CNT [30]. (b) Cartoon illustration of the osmotic stress method showing coexistence of the assembled DNA-CNT phase and the osmolyte phase. (c) XRD profiles (symbols) of the DNA-CNT phase equilibrated against 10% and 50% PEG8k (weight/weight) in 150 mM NaCl $1\times \mathrm{TE}$ $p\mathrm{H}$ 7.5, respectively. Error bars of $Q$ and $I(Q)$ are smaller than the sizes of symbols. Here $Q=4\pi \sin (\theta )/\lambda$ is the scattering vector, where $2\theta$ is the scattering angle and $\lambda$ is the x-ray wavelength. Both peaks are fit with Lorentzian functions (solid lines) giving comparable peak widths of $0.033{\AA }^{-1}$ (after correction by instrument resolution of $0.006{\AA }^{-1}$).

Figure 2

Measured force-distance curves of DNA-CNT hybrids and calculations based on electrostatic theories. The force is given by the osmotic pressure $\Pi$ in Pascal. Uncertainties for inter-hybrid distances range between 0.15 and 0.35 Å. The concentrations of PEG8k were measured by weight to accuracy better than 0.1% and calculations of pressure $\Pi$ used well-established parameters [22]. Both error bars are thus smaller than symbols. In (a), as-measured experimental data are shown as symbols. Solid lines show the calculated force-distance curves using the cylindrical cell model with the DNA-CNT’s diameter taken as 28 Å. Note that the rightmost data point for each curve represents the lowest PEG8k concentration needed to condense DNA-CNTs, e.g., 20% PEG8k ($\Pi \sim 8\mathrm{atm}.$) in 50 mM NaCl and 5% ($\Pi \sim 0.5\mathrm{atm}.$) in 150 mM NaCl. In (b), the high-pressure (i.e., short-distance) region is zoomed in to illustrate the crossovers between experimental data and theoretical calculations, illustrating the different slopes between experiment and theory.

Figure 3

Measured force-distance curves of DNA-CNT and dsDNA and fits based on the hydration force formalism. In (a), the same experimental data as in Fig. 2a are shown, except that the curves for dsDNA are offset by adding 8 Å to the interhybrid distance. In (b), symbols show the same data as in Fig. 2a; solid lines show the fits using two exponentials including the hydration and electrostatic forces.