Programmable DNA origami subunits

DNA origami is an experimental technique by which one can create intricate, 3D structures on the nanometer scale that are composed entirely of DNA. This process is done by taking a long single-stranded DNA loop (in our lab we use an 8064 base long plasmid derived from the M13mp18 phage) and combining it with short DNA oligomers that are usually 30 to 60 bases in length; these pieces of DNA are respectively called the scaffold and staple strands. By having staple strands that are complementary to disparate regions of the scaffold, those regions will be brought physically close together in space, thus ‘folding’ the scaffold strand into different target geometries.

We want to use DNA origami to create new classes of colloidal subunits for self-assembly, which enable a higher degree of control than has typically been achieved using DNA-coated colloids or patchy particles. Inspired by the self-limited assembly of biological structures, like viral capsids and microtubules, our lab creates DNA origami subunits that have controllable dihedral angles and specific interactions. At the moment we are currently studying the assembly of tubules from rigid triangular subunits that interact via shape-complementary lock and key binding.

To see the outcome of assembly we typically use three measurements: epi-fluorescence microscopy, negative stain transmission electron microscopy (TEM), and cryogenic-EM. Each of these serves to give different information about the outcome of our assemblies on different length scales. We use fluorescence microscopy to see the lengths of the tubules or study how they grow over time. With TEM we get microscopic details about individual tubules that form. Finally, cryogenic-EM lets us assess the structure of the individual DNA origami subunits on the scale of the double helix.

Our experiments are complemented by computation and theoretical modeling. For example, computer simulations extract physical parameters from our experimental systems that are otherwise difficult to measure directly, like the bending modulus of our origami subunits. Modeling and computer simulations also help to reveal the mechanisms that govern the polymorphic distribution of tubules that form in experiment.

References

Geometrically programmed self-limited assembly of tubules using DNA origami colloids, Daichi Hayakawa, Thomas E. Videbæk, Douglas M. Hall, Huang Fang, Christian Sigl, Elija Feigl, Hendrik Dietz, Seth Fraden, Michael F. Hagan, Gregory M. Grason, and W. Benjamin Rogers PNAS 119 (43) e2207902119 (2022)

Tiling a tubule: how increasing complexity improves the yield of self-limited assembly, Thomas E. Videbæk, Huang Fang, Daichi Hayakawa, Botond Tyukodi, Michael F. Hagan and W. Benjamin Rogers, J. Phys.: Condens. Matter 34 134003 (2022)