Polymer tube nanoreactors via DNA-origami templated synthesis

We describe the stepwise synthesis of precise polymeric objects programmed by a 3D DNA tube transformed from a common 2D DNA tile as a precise biotemplate for atom transfer radical polymerization.


Materials and instruments
All solvents and reagents were purchased from commercial sources and were used without further purification.
All solvents and chemicals were purchased from commercial sources and were used without further purification. DNA staple strands and ATRP initiator modified DNA (DNA-initiator) were either synthesized by 12-Column DNA Synthesizer from POLYGEN GmbH and purified by Agilent 1260

Transformation to DNA tube
To DNA tile (0.5 pmol) solution was added a set of folding DNA strands (250 pmol each) and the mixture was incubated at 32 degree for overnight. The obtained DNA tube was pourified again with PEG precipitation method.

Transmission electron microscopy (TEM)
5 uL of sample (1 nM) was applied on carbon coated copper grid with hydrophilic treatment. After 10 minutes incubation, the remaining solution was removed and the sample grid was stained with 2 % uranyl formate solution for 20 seconds. The stained grid was washed with filtered water for three times and dried in air. Imaging was done with JEOL 1400 instrument and obtained images were analyzed by ImageJ software.

Dynamic and static light scattering (DLS and SLS)
Light scattering measurements were performed with an ALV/CGS3 compact goniometer system with a He/Ne laser (632.8 nm), ALV/LSE-5004 multiple-tau full-digital correlator and ALV5000 software. For temperature controlled measurements, the light scattering instrument was equipped with a thermostat from Julabo. Measurements were performed at 20 °C at 13 angles ranging from In dilute solutions, the relaxation rate Γ(q)=1/τ(q) is usually diffusive defining the diffusion For species with small size R i.e., , both the scattering intensity I(q) and D=D 0 are q-independent with I ~ cM and D 0 =k B T/(6πη 0 R h ) where c, M, R h , η 0 , k B , and T are the probed species concentration, its molecular weight and hydrodynamic ratio, the solvent viscosity, the Boltzmann constant and the absolute temperature, respectively. For qR ~ 1, both I(q) and D(q) depend on q defining the probing length (2π/q). The former, known as the form factor, yields (at low qR g ) the radius of gyration R g , whereas the effective D is given by, with A is a parameter characterizing the shape of the diffusing species.

Supplementary figures and tables
Figure S1 DNA tile. The design of DNA tile [3] and the position of DNA handles to attach ATRP initiator moieties (dark blue circle) chosen from Cadnano software. [4] The details of all staple strand DNA sequences are listed in Table S2. Table S1 Summary of dimensions of the DNA tile, DNA tube, polymer tube, G4-incorporated DNA tube before / after ATRP (G4-tube / G4-polymer tube) from theoretical, AFM, and DLS. Figure S7 ABTS activity of DNAzymes in polymer tubes before / after nuclease addition (50 mU). 80 % of the DNAzyme activity was maintained even in nuclease presence.
15 Table S2 Detail of staple DNA sequences. Each number corresponds to the position shown in Figure   S1. The Sequences extended with sticky DNA handle sequence at 3' are named as "3stX (X = position number)". Folding DNA sequences to transform DN tile to DNA tube are named as "FX".
For preparing DNAzyme-introduce DNA tile, the sequences are separated into DNA handleextended part (3stX half) and DNAzyme-extended part (g4-X half)