Liquid crystal phase behavior of a DNA dodecamer and the chromonic dye Sunset Yellow

Sunset Yellow (SSY) is an aromatic heterocycle nano-sheet functionalized by hydrophilic sulphanate groups. SSY forms chromonic stacks and liquid crystal (LC) phases in aqueous solution. The DNA oligomer 5′-GCGCTTAAGCGC-3′ is a self-complementary strand which forms duplexed B-form helices in aqueous solution, which, similarly, aggregate into chromonic stacks and form LC phases. Binary aqueous solutions of these two molecules were investigated using polarized optical microscopy, x-ray diffraction, and spectroscopy. At lower solute concentrations and/or higher temperatures these solutions form uniformly mixed single phases, including isotropic, chiral nematic, and hexagonal columnar LCs. At higher solute concentrations and/or lower temperatures, the uniform columnar solution separates into two columnar phases, one containing SSY with trace DNA and the other containing both SSY and DNA aggregates. The study of these solutions indicates that the mixed and unmixed phases are composed of single component SSY or DNA chromonic stacks, with the DNA stacks containing a small fraction of intercalated SSY, evidenced by structurally induced circular dichroism in the SSY absorption band. In the columnar monophase, the hexagonal lattice sites are occupied randomly by either DNA or SSY columns, with the column spacing varying continuously with the SSY-DNA mass ratio. The results demonstrate significant selectivity in the chromonic stacking of both molecules. The binding mode of these chromonic LCs may have applications to adaptive optics and nucleic acid chemistry.

Figure 1

Chemical structure of (a) SSY and (b) Guanine (left) hydrogen bonded to Cytosine (right). The aromatic heterocycles (orange) lie in the plane of the paper. (c) rDD sequence duplexed to rDD sequence.

Figure 2

(a–c) POM textures with concentration increasing from left to right at room temperature. (a) Pure SSY (${\mathrm{mf}}_{ssy}=1$) in $I, N$, and $M$. (b) Pure rDD ${\mathrm{mf}}_{ssy}=0$ in N*, $M$, and $M_2$. (c) Mixture at ${\mathrm{mf}}_{ssy}=0.57$ in N*, $M$, and $M_s$. (d) POM textures at selected temperatures during heating of ${\mathrm{mf}}_{ssy}=0.57$ with a transition from $M_s$ to $M$.

Figure 3

$d$ (left axis) and coherence length (right axis) as a function of temperature for ${\mathrm{mf}}_{ssy}=1/3$ and $c=522$ mg/mL during cooling. The inset plot shows the corresponding fitted Lorentzian peaks in $Q$ space.

Figure 4

$d$ as a function ${\mathrm{mf}}_{ssy}$ in $M$. The values of $d$ were extrapolated to $c=462$ mg/mL using the relationship in Eq. (2). This linear relationship indicates that the two molecules segregate into homogeneous columns that are mixed randomly at the hexagonal lattice sites. The inset figure shows a simplified $M$ lattice with $d$ and $h$ labeled.

Figure 5

Fitted Lorentzians for the XRD peaks in the columnar range for ${\mathrm{mf}}_{ssy}=2/3$ and $c=562$ mg/mL during heating. There are two peaks corresponding to the different spacing in the SSY rich and the rDD domains until $86{}^{\circ }\mathrm{C}$ where the domains mix and return to a single column spacing in $M$.

Figure 6

(a) Phases of rDD-SSY mixture as a function of concentration, ${\mathrm{mf}}_{ssy}$, and temperature at four selected mass fractions. The plane at $20{}^{\circ }\mathrm{C}$ is extruded beneath in (b) where the phases of rDD-SSY are shown as a function of concentration and ${\mathrm{mf}}_{ssy}$.

Figure 7

Smoothed (a) CD and (b) absorbance spectra of rDD-SSY mixtures. $\left[\mathrm{SSY}\right]=0.5$ mg/mL. [rDD] in mg/mL are labeled on the respective curves. CD spectra has saturated by $\left[\mathrm{rDD}\right]=150$ mg/mL. Only SSY absorbs in this domain, indicating that the achiral SSY molecules are binding to the chiral rDD duplexes. These solutions are $I$.

Figure 8

Ellipticity at 490 nm during heating at $2{}^{\circ }\mathrm{C}$/min for $\left[\mathrm{SSY}\right]=0.5$ mg/ml and $\left[\mathrm{rDD}\right]=150$ mg/ml. The inset graph shows smoothed CD spectra and the background signal during cooling. The handedness switches from right to left during cooling. Above $79{}^{\circ }\mathrm{C}$, the induced CD weakens due to dissociation of the SSY from the rDD.