Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction

Abstract

While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.

Figure 1

Molecular designs of squaraine–HJ constructs with three different linker lengths: short (green), medium (med; blue), and long (magenta). (a) General procedure for oligonucleotide postmodification with a squaraine dye depicting chemical structures of the resulting squaraine-labeled thymidines, linkers tethering squaraines to thymidines, and bis(chloroindolenine)squaraine. (b) Schematics of dimers with unequal linkers tethered to immobile HJ. (c) Schematics of dimers with equal linkers tethered to immobile HJ. (d) Schematics of monomers with varying linker lengths tethered to immobile HJ. The strands of immobile HJ are labeled A, B, C, and D.

Figure 2

Steady-state absorption and circular dichroism of squaraine monomers and dimers tethered to HJ. The spectra were recorded in 1× TBE, 15 mM MgCl₂ at room temperature. The concentrations of squaraine–DNA constructs were 1.5 μM. (a) Absorption profiles of single bis(chloroindolenine)squaraine covalently attached to strand A of HJ (i.e., monomers) do not show dependence on the length of the linker. (b) CD spectra of achiral bis(chloroindolenine)squaraine covalently attached to strand A of HJ (i.e., monomers) do not exhibit an induced CD signal. (c) Absorption profiles of dimers with equal linkers are blue-shifted relative to the monomers, indicative of the presence of excitonic coupling. (d) CD profiles of dimers with equal linkers show exciton-coupled CD signals with low amplitude. (e,g,i) Absorption profiles of dimers with unequal linkers are blue-shifted relative to the monomers, indicative of the presence of excitonic coupling. (f) CD profile of dimers B^medC^long and B^longC^med show exciton-coupled CD signal with low magnitude. (h,j) CD profiles of dimer pairs B^longC^short/B^shortC^long and B^medC^short/B^shortC^med show high-magnitude exciton-coupled CD signals of opposite handedness.

Figure 3

Changes in molar CD profiles of squaraine dimers upon incremental addition of the paired dimer with interchanged linkers._. (a) Stepwise addition of dimer B^shortC^long [10× (2 μM, 10 μL)] to dimer B^longC^short (2 μM, 100 μL) results in the CD profile similar to that of (BC)^med. (b) Stepwise addition of dimer B^shortC^med [10× (2 μM, 10 μL)] to dimer B^medC^short (2 μM, 100 μL) results in the CD profile similar to that of (BC)^short. All measurements were performed in 1× TBE, 15 mM MgCl₂ at room temperature.

Figure 4

Schematic representation of the influence of linker length on an equilibrium between isomers of the stacked HJ covalently templating squaraine dimers. The transitional open conformation of HJ is not shown. (a) Unlabeled HJ at the dynamic equilibrium between Iso I and Iso II isomers. (b) Iso I and Iso II are equally favorable when dyes are covalently tethered to the HJ via equal-length linkers resulting in a racemic mixture of dimer enantiomorphs. (c) Noncovalent binding of dye dimer to the HJ arm in Iso I and Iso II isomers that feature opposite base pairing. (d,e) A shift in equilibrium toward a dominant HJ isomer when dyes are covalently tethered to the HJ via unequal-length linkers. A dominant isomer is the isomer where a dye–dye distance is shorter [i.e., Iso I in (d) and Iso II in (e)].

Figure 5

KRM-derived dimer geometries with unequal length linkers are shown in pairs as mirror images: B^shortC^med/C^medB^short and B^shortC^long/B^longC^short. The left schematic defines the geometric parameters of the alignment between TDMs 1 and 2 in each dimer: a center-to-center distance R in Å, slip angles θ₁° and θ₂°, and an oblique angle α°. Note that the fitting procedure determines the position and orientation of TDM that aligns with the long axes of the squaraine dye but not the rotation of the dye core around its long axis. As such, the dye core rotations were arbitrarily chosen.