Supramolecular assembly of phenanthrene–DNA conjugates into light-harvesting nanospheres

The self-assembly of highly functionalized phenanthrene–DNA conjugates into supramolecular nanostructures is presented. DNA oligomers modified with phenanthrene residues at the 3′-end and internal positions self-assemble into spherical nanostructures. The nanospheres exhibit light-harvesting properties. Upon irradiation of phenanthrene, the excitation energy is transferred along phenanthrene units, resulting in phenanthrene–pyrene exciplex formation.


General Methods
All reagents and solvents were purchased from commercial sources and used without further purification.The phenanthrene and pyrene phosphoramidites used in the solid-phase synthesis were synthesized according to published procedures. 1,2Water was used from a Milli-Q system.Mass spectra were measured by the Analytical Research and Services (ARS) of the University of Bern, Switzerland, on a Thermo Fisher LTQ Orbitrap XL using Nano Electrospray Ionization (NSI).All mass spectra were measured in negative ion mode in mixtures of acetonitrile/water/triethylamine.UV-vis spectra were measured on a Jasco V-730 spectrophotometer using quartz cuvettes with an optical path of 1 cm.Fluorescence spectra were recorded on a Jasco spectrophotometer FP-8300 using an excitation and emission slit of 2.5 nm.The fluorescence quantum yield was determined according to the published procedure 3 relative to quinine sulfate in 0.5 M H2SO4. 4upramolecular self-assembly was performed via thermal disassembly (heating to 75 °C) and assembly (cooling 0.5 °C/min to 20 °C) in a thermostat equipped with a Peltier.Doping experiments were conducted by replacing 1*2 with 1*3 while keeping a constant hybrid concentration of 1 µM.After each addition, the nanostructures were reassembled as described above (heating to 75 °C and cooling to 20 °C) to integrate the added strands into the aggregates.Dynamic light scattering (DLS) experiments were performed on a Malvern Zetasizer Nano Series instrument (λ = 633 nm) in particle size distribution (PSD) mode (number value) at 20 °C.Atomic force microscopy (AFM) experiments were measured on a Nanosurf FlexAFM instrument under ambient conditions using tapping mode.AFM samples were prepared on (3-aminopropyl)triethoxysilane (APTES)-modified mica sheets (Glimmer "V1", 20 mm x 20 mm, G250-7, Plano GmbH) according to published procedures. 1,5Samples for cryo-EM were plunge-frozen using the FEI Vitrobot Mark 4 at room temperature and 100% humidity.In brief, copper lacey carbon grids were glow discharged (air -10 mA for 20 seconds).Then, 3 L of the sample were pipetted on the girds, blotted for 3 seconds, and plunged into liquid ethane.The sample grids were stored in liquid nitrogen.Images were measured with a Gatan 626 cryo holder on a Falcon III equipped FEI Tecnai F20 in nanoprobe mode.Due to the nature of the sample, acquisition settings had to be adjusted for a low total electron dose (less than20 e -/Å 2 ) using EPU software.The diameters of the nanostructures were measured in Fiji 6,7 using the multi-point tool to set marks.
Equation S1 Formula used to calculate the FRET efficiencies   .

Figure S2
Figure S2 Mass spectrum of 1.

Figure S6
Figure S6 Mass spectrum of 3.

Figure S7
Figure S7 Mass spectrum of 3.

Figure
Figure S9 (a) UV-Vis absorption of 1*2 at 250 nm during assembly and disassembly: cooling from 75 °C to 20 °C (blue) and heating back from 20 °C to 75 °C (red) (b) temperature-dependent UV-vis absorption spectra of 1*3 disassembled at 75 °C (red) and self-assembly at 20 °C (blue), and (c) absorbance of 1*3 at 250 nm during assembly and disassembly: cooling from 75 °C to 20 °C (blue) and heating from 20 °C to 75 °C (red).Conditions: 1 µM each single strand, 10 mM sodium phosphate buffer pH 7.2, 0.10 mM spermine tetrahydrochloride, 20 vol% ethanol, heating and cooling gradient 0.5 °C•min -1 .3,6-Dialkynylphenanthrene, 2,7-dialkynyl phenanthrene and 1,8-dialkynyl pyrene units in 1*2 and 1*3 absorb at 260 nm and 250 nm (Fig.S8, UV-vis spectra of the representative diols in ethanol).Therefore, the UV-Vis absorption measurements of 1*2 and 1*3 during the assembly and disassembly process at 250 nm represent a combination of the DNA assembly and the change of absorption of the modifications due to the assembly.The measurements were conducted at 250 nm instead of the usual 260 nm for DNA hybridization to reduce the effect of the changes in the absorption by the modification.

Table S3
Summary of diameters measured in cryo-EM images, AFM images and DLS.The reported distances are mean values with the corresponding standard deviation and the number of measurements (n) is indicated in the brackets.Duplex Size Diameter (nm) Z-Average Size Diameter (nm) PDI PDI width (nm) Count Rate (kcps) Attenuator

Table S4
*  is the integral of the emission of 1*2 ⦁   is the concentration of the donor ⦁   *  is the concentration of donor in 1 µM 1*2 (6 µM)Equation S3 Equation used to calculate   .=   *  •   *  +   *  •   *    *  is the number of donors in 1*2 (6) ⦁   *  is the concentration of 1*2 ⦁   *  is the number of donors in 1*3 (5) ⦁   *  is the concentration of 1*3Equation S4 Formula to calculate the number of donors involved in FRET to one acceptor (  ).Formula used for the calculation of the number of duplexes involved in the excitation of one acceptor   .At different fractions of 1*3 (c1*3) and 1*2 (c1*2): concentrations of donor (cD) and acceptor (cA), calculated fluorescence emission integrals of donor in the absence of the acceptor (FD), deconvoluted fluorescence emission integrals of the donor in presence of the acceptor (FDA), FRET efficiencies (EFRET) and number of donors (ND) and duplexes (NDuplex) involved in FRET to one acceptor.All measurements are mean values of three measurements and the corresponding errors are indicated.Conditions: 0.99−0.50µM 1*2, 0.01−0.50µM 1*3, 10 mM sodium phosphate buffer pH 7.2, 0.10 mM spermine tetrahydrochloride, 20 vol% ethanol, λex.330 nm.