Folding and Characterization of a Bio-responsive Robot from DNA Origami

Summary

DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here we describe a protocol for the folding of a bio-responsive robot from DNA origami, its purification and negative staining for transmission electron microscopic imaging (TEM).

Abstract

The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both stimuli and cargo can be tailored according to specific needs. Here we describe the DNA nanorobot fabrication protocol, with the use of the DNA origami technique. The procedure initiates by mixing short single-strand DNA staples into a stock mixture which is then added to a long, circular, single-strand DNA scaffold in presence of a folding buffer. A standard thermo cycler is programmed to gradually lower the mixing reaction temperature to facilitate the staples-to-scaffold annealing, which is the guiding force behind the folding of the nanorobot. Once the 60 hr folding reaction is complete, excess staples are discarded using a centrifugal filter, followed by visualization via agarose-gel electrophoresis (AGE). Finally, successful fabrication of the nanorobot is verified by transmission electron microscopy (TEM), with the use of uranyl-formate as negative stain.

Introduction

The uses for nucleic acids nanotechnology are astounding. The tractability of the Watson-Crick base pairing as well as the ease and relative low-cost of large-scale synthesis of custom-made oligos² has generated an explosion of applications³ and research in the field of DNA nanotechnology. Structural DNA nanotechnology, based on the immobile Seeman junction^4,5 as a fundamental building block makes use of DNA as a self-assembling elementary unit for the construction of arbitrary shapes^6-8.

The recent development of the scaffolded DNA origami⁹ technique allows for the construction of complex 2D/3D nano-architectures^10-12 with sub-nanometer precision and is an efficient route for building new functional objects with increasing complexity and astonishing diversity. The construction process is based upon a long scaffold single stranded DNA, usually derived from a viral genome, which can be folded through the hybridization of hundreds of short single strand DNA oligos termed staples. The high structural resolution obtained by this technique is the direct result of the natural dimensions of the DNA double helix, while the reproducibility of fabrication is the result of tailoring the short single-strand staple sequences to facilitate the maximum hydrogen-bonding complementarity achievable. With the use of a slow temperature annealing ramp the designed lowest-energy, thermodynamically preferred nanostructure is reached in high yields and fidelity. The easy implementation of junction design rules in a computer code enabled the development of CAD tools, such as caDNAno¹³, that extremely simplify the task of designing large, complex structures containing hundreds of connected junctions.

Previously we described the design of a DNA nanorobot with the aid of the caDNAno tool^14,15. Here we depict the fabrication and visualization, via transmission electron microscopy (TEM), of the nanorobot, a 3D hollow hexagonal nanodevice, with dimensions of 35 x 35 x 50 nm³, designed to undergo a major conformational change in response to a predetermined stimuli and present specific cargo, such as proteins or nucleic acid oligos, sequestered inside. While 12 loading stations are available inside the hollow chassis, the actual number of bound cargo differs with cargo size. Cargo molecules range from small DNA molecules to enzymes, antibodies and 5-10 nm gold nanoparticles. Cargocan either be uniform or heterogeneous, such that each nanorobot contains a mixture of different molecules. Sensing is achieved via two double helical locking gates design to sense proteins, nucleic acids or other chemicals, based either on aptasensor^16,17 or DNA strand displacement¹⁸ technologies. Recent developments in aptamer selection protocols^19-21 enable the design of nanorobots responding to an ever increasing range of molecules and cell types.

Earlier work showed a nanorobot carrying a specific antibody, which upon binding to its antigen can relay either an inhibitory or a prolific signal to the inside of specific cell types in a mixed cell population¹⁵. An exciting feature of these nanodevices is their ability to perform even more complex tasks and logic control with the introduction of different nanorobot subtypes in a single population. Recently we demonstrated specific subtypes of nanorobots performing as either positive or negative regulators, controlling an effector population containing an active cargo molecule²².

The protocol presented here describes the fabrication, purification and imaging of a nanorobot gated with aptamer sensor sequences which bind selectively to PDGF to facilitate the opening of the nanorobot^15,22. The fabrication process described is similar to the nanorobot fabrication process initially depicted by Douglas et al.¹⁵ with changes aimed at reducing overall process duration, while increasing the yield and purification rates.

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Protocol

1. Preparation of Staples Pool Mixture

1. Order lyophilized DNA nanorobot staples on 96-well plates as listed in Table 1 (see Materials) and normalize to 10 nmol. For a detailed description of the design and architecture of the DNA nanorobot see Ben-Ishay et al.¹⁴ and Douglas et al.¹⁵).
2. Reconstitute each staple well with DNase/RNase-free ultrapure to a concentration of 100 µM. For staples normalized to 10 nmol, reconstitute with 100 µl of ultrapure water.
3. Pool together 20 µl of each staple using a multichannel pipettor and a sterile 55 ml solution basin.
   Note: Since the nanorobot shape is comprised of 254 staple strands (including Core, Edges, Handles and Guides sequences, Table 1), the concentration of each of the staples in the staples pool is 394 nM. Removing staples from the staple pool, or adding some at different volumes, may reduce the yield considerably, or otherwise result in unfolded aggregates.

2. Preparation of Fabrication Reaction Mixture

1. For a standard reaction mixture use 40 µl of M13mp18 viral genome circular single strand DNA, corresponding to 4 pmol of scaffold DNA (100 nM stock solution, see Materials). Final concentration of scaffold in the fabrication mixture is 20 nM, final volume 200 µl.
   1. Adjust the amount of scaffold DNA according to specific needs; however, keep the final concentration of scaffold DNA in the reaction mixture at a constant 20 nM.
2. Add staples to reach a scaffold to staples ratio of 1 to 10, respectively. For a 20 nM scaffold DNA concentration, each of the 254 staples’ final concentration is 200 nM. For a 200 µl final reaction volume add 102 µl of the staples pool mixture (section 1.2).
   1. Add specific Gate sequences separately to the folding reaction mixture at this time. These oligos are ordered separately and require HPLC purification. Ensure that Gate oligos are present in a 1:10 scaffold to Gate sequence ratio, i.e. 200 nM of each oligo for a 20 nM scaffold concentration. For a 200 µl folding reaction volume, add 0.4 µl for each of the four Gate oligo at a 100 µM stock concentration.
3. Add 10x TAE stock buffer to reach a final concentration of 1x TAE (40 mM Tris-Acetate, 1 mM EDTA). For a 200 µl folding reaction volume, add 20 µl of 10x TAE.
4. Add 1 M MgCl₂ to a final concentration of 10 mM. For a 200 µl folding reaction volume, add 2 µl of 1 M MgCl₂.
5. Add 36 µl of DNase/RNase free ultrapure water to a reach a final volume of 200 µl.
6. Vortex and aliquot 100 µl samples into PCR vials.
   Note: Consult thermal cycler specification regarding the maximum reaction volumes to be used. Reducing the volume to meet these limits will not reduce the yields obtained. Reaction volumes above the maximum specified will jeopardize the yields.

3. Temperature Annealing Ramp of Fabrication Reaction

1. Program thermal cycler as followed:
   1. Ramp 85 °C to 60 °C at a rate of 5 min/°C.
   2. Ramp 60 °C to 4 °C at a rate of 75 min/°C.
   3. Hold at 4 °C indefinitely.
2. After fabrication has ended store samples at -20 °C.

4. Removal of Excess Staples

1. Add 100 µl of folding reaction mixture to a 0.5 ml centrifugal filter with a MWCO of 100 kDa. Save a 10 µl sample of nanorobots pre-purification for later analysis.
2. Centrifuge for 10 min at 9,600 x g.
3. Add 400 µl of folding buffer (1x TAE, 10 mM MgCl₂).
4. Repeat steps 4.2 and 4.3 twice more.
5. Centrifuge for 5 min at 9,600 x g.
6. Recover the concentrate by placing the filter upside down in a clean microcentrifuge tube and spin for 1 min at 9,600 x g. Final volumes may vary depending on the initial volume of fabrication reaction mixture that was put into the filter. Typically a 25-60 µl final volume of concentrated nanorobot sample is obtained.
7. Measure concentration of DNA in the samples via spectrophotometer at 260 nm. Use molecular weight of 5.3 µg/pmol when calculating molar concentrations of nanorobot samples.
   Note: The molar extinction coefficient for dsDNA, 50 µg/OD_260, is sufficient for most applications. 48 µg/OD₂₆₀ takes into account the poly thymine ssDNA stretches at the Edges staples.

5. Agarose Gel Electrophoresis Analysis of Folded Nanorobots

1. Preparation of 0.5x TBE (45 mM Tris-Borate, 1 mM EDTA), 2% agarose gel supplemented with 10 mM MgCl₂ (adapted from Ernesto Castro et al.²¹):
   1. Prepare 0.5x TBE buffer by diluting 6.25 ml of 10x TBE stock buffer in 118.75 ml of ddH₂O.
   2. Dissolve 2.5 g of agarose in 125 ml of 0.5x TBE buffer.
   3. Boil in microwave until the agarose is completely dissolved.
   4. Add 1.25 ml of 1 M MgCl₂ to final concentration of 10 mM.
   5. Add 7 µl of 10 mg/ml ethidium bromide.
   6. Wait for solution to slightly cool and fill the gel tray before the agarose gel solidifies. Install desired comb immediately.
   7. Prepare 1 L 0.5x TBE running buffer by adding 50 ml of 10x TBE stock buffer and 10 ml of 1 M MgCl₂ to 940 ml of ddH₂O.
   8. Once gel is solid add running buffer to the electrophoresis device and put device in an ice bath.
2. Load 1 µg total DNA of the nanorobots pre-purification (step 3.2), and post purification (step 4.7), alongside a scaffold DNA sample and a 1 kb DNA marker, onto the gel. An example is given in Figure 2. Actual volumes of samples depend on the concentrations obtained after purification. Each samples is loaded with loading buffer at a 1:6 final volume ratio.
3. Set power source to 80 V and run gel for 3 hr. Run the gel in a bath filled with ice and water. Nanorobots will unfold and appear as a smear if the agarose gel heats up during electrophoresis. During electrophoresis add additional ice to keep device from heating.
4. View gel on a UV table (Figure 2).

6. Negative Stain of Nanorobot with Uranyl-formate

1. Preparation of 2% uranyl-formate stock solution (adapted from Castro et al.²³):
   1. Weigh 100 mg of uranyl-formate powder into a 15 ml tube.
   2. Boil DNase/RNase free ultrapure water for 3 min to de-oxygenate.
   3. Add 5 ml of deoxygenated hot water (~60 °C) into the 15 ml tube containing the uranyl-formate powder (from previous step). Tightly close lid, wrap in aluminum foil and vortex rigorously for 10 min (fasten tube to a vortex). Solution should appear turbid with a yellow color.
   4. Filter solution through a 0.2 µm syringe filter. Solution should become clear.
   5. Aliquot 200 µl of the solution into microcentrifuge tubes.
   6. Centrifuge at max speed for 5 min in a table top centrifuge to pool samples at the bottom of the tube.
2. Loading of sample to grid and negative staining:
   1. Defrost a 200 µl aliquot of 2% uranyl-formate solution (prepared in section 6.1). Add 10 µl of 0.5 M NaOH solution and vortex rigorously for 3 min. Centrifuge at max speed for 5 minutes using a table top centrifuge.
   2. Meanwhile, glow-discharge grid using room air at 0.2 mbar and 25 mA for 30 sec.
   3. Add 15 µl of 2 nM nanorobot sample after purification (section 4.7) onto topside of grid (held with forceps) and let absorb for 1 min. Use filter paper to drain the excess liquid by placing the grid on top of the filter paper. Do not touch the grid surface.
   4. Add 10 µl of the 2% uranyl-formate (from step 6.2.1) onto the topside of grid (held with forceps).
   5. Quickly use filter paper to drain the excess liquid by placing the grid on top of the filter paper. Do not touch the grid surface.
   6. Repeat steps 6.2.4 and 6.2.5.
   7. Add 10 µl of the 2% uranyl-formate (from step 6.2.1) onto the topside of grid (held with forceps). Let staining solution absorb for 30 sec.
   8. Use filter paper to drain the excess liquid by placing the grid on top of the filter paper. Do not touch the grid surface.
   9. Let the grid dry completely for at least 30 min, face up on a filter paper, before injecting into the TEM.

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Results

Representative results are shown in Figure 2A. All lanes contain 1 µg of total DNA, measured via spectrophotometer (OD₂₆₀). Compared with the circular single-strand DNA scaffold (Lane 2), nanorobots are hindered in the gel due to their higher molecular weight, the result of staples hybridization to the scaffold DNA (Lane 3. Red arrow). The low molecular weight band in Lane 3 represents excess staples which did not bind to the scaffold DNA (Green arrow). After purification via centrifugal ...

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Discussion

We described the fabrication, purification, and visualization of the DNA nanorobot. Following fabrication of the hexagonal chassis of the device, the function of the nanorobot is programmed with the simple introduction of specific cargo and sensing strands to the robot which readily find their designated position due to hydrogen-bonding complementarity with available single-strand docking sites^14,15,22.

The fabrication protocol described uses a slow annealing ramp, which is generall...

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Materials

Name	Company	Catalog Number	Comments
DNase/RNase free distilled water	Gibco	10977
M13mp18 ssDNA scaffold	NEB	N4040S
10x TAE	Gibco	15558-042
1 M MgCl2	Ambion	AM9530G
Amicon Ultra 0.5 ml centrifugal filter 100K MWCO	Amicon	UFC510024
Agarose	Promega	V3125
TBE buffer	Promega	V4251
Ethidium bromide 10 mg/ml solution	Sigma Aldrich	E1510
1 kb DNA marker	NEB	N3232S
Loading Dye	NEB	B7021S
uranyl formate	polysciences	24762
carbon-coated TEM grids	Science services	EFCF400-Cu-50
Thermal Cycler c1000 Touch	Bio-Rad
Glow Discharge K100X	Emitech
UV table Gel Doc EZ Imager	Bio-Rad
NanoDrop 2000c	Thermo Scientific
TEM FEI-G12	Tecnai