Architecting DNA – The Ke Lab

In 2006, a few hundred years after origami delighted courtiers of the Edo period, a derivative art form took centerfold in Nature magazine: DNA origami. Like paper origami, folded painstakingly from single leaves of paper, DNA origami are continuous assemblages, folded from a lone, long single-stranded scaffold, about seven thousand kilobases in length. Origami architects design scaffolds that fold into a diverse topiary of target shapes, guided by complementary interactions with short, synthesized staple strands. This nanoscale origami has myriad applications, including drug delivery and DNA computing. Assembly of target shapes is straightforward, and reads like a recipe for roux: combine scaffold strands and staple strands over a low simmer.

Examine the results a few days later, and you can find nanometer-high monoliths scattering the field of an atomic force microscope, like Stonehenge toppled by a giant’s finger.

In 2018, the contemporary epicenters of DNA folding are far removed from Japan. The Wyss Institute in Cambridge, MA is perhaps the most famous, and one of its notable alumni, Dr. Yonggang Ke, is now an assistant professor in the employ of the Wallace H. Coulter Department of Biomedical Engineering. In recent years, Dr. Ke has been steering his own nanoengineering lab towards novel DNA folding techniques and applications. Ke is perhaps best known for his work on DNA brick, which bear structural likeness to LEGO brick, and captured the imagination of the world in 2012. A DNA brick comprises very short strands of DNA, only 32 nucleotides long. Thousands of these bricks can undergo self-assembly into a target 3D structure. They have two advantages over DNA origami: bricks can bind together independently and are chemically synthesized in their entirety.

Nanoarchitecture is in its first blush, its youth evident in the design choices of Ke and collaborators, which tend often towards the whimsical: teddy bears feature in his oeuvre, as do low-resolution maps of the Americas. However, a very curious feature of this molecular masonry is that its structures are assembled not in positive, but in negative space. It is not a teddy bear Ke produced, but the impression of a teddy bear, a cavity charmingly wrought into a solid cube of bricks.

This cavity’s topology can interact precisely with other molecules’ surfaces, enabling more precise cartography and functional understanding of otherwise complex and inscrutable proteins.

Elsewhere in the Ke lab, synthetic RNAs are directing assembly of viral protein onto DNA nanostructures. These counterfeits of native RNAs serve as ‘origin-of-assembly,’ or docking, sites for viruses in vivo. These sites, which initiate protein subunit assembly, are distributed like toeholds along the pre-assembled DNA nanostructure. From each toehold, the RNA scaffold spirals upward like long, sticky lichen, and the protein subunits assemble into rank along the scaffold, resulting in blooms of viral capsids adhered to the DNA nanostructure. These capsids, the polyhedral shells that normally envelop viral genomes, are perfectly folded, and perfectly hollow, suggestively devoid of genetic material. Could this make capsids cultivated on DNA nanostructures a prime vector for delivering drugs into human cells? Drug delivery is an application Dr. Ke has explored in a recent paper which investigated the uptake of DNA nanostructures into cells. The nanostructures can cross the cell membrane, but once in, they lack the clearance from the cell to be disseminated into the cytosol proper. The foray into clinical application is unusual for the lab, which, being highly experimental, aims to show that certain novel techniques can work, in order that other groups can put them to the clinical yoke.

The sterile hollowness of the capsid provokes another question, especially in light of the quest to create a synthetic genome: could DNA nanostructures have the potential for self-replication? To imbue a synthetic structure with the basic tenet of life – it is what Gepetto wished for Pinocchio. Dr. Ke allows that no architected DNA nanostructures are known to replicate themselves. Yet for the sake of example, he explains how a sort of self-replication could in theory be achieved. He conjures up two imaginary structures, A and B. Imagine that structure A is a kind of selfish enzyme; with zealot’s fervor, it catalyzes the conversion of structure B into structure A, until B is completely spent. The once-heterogeneous population of As and Bs is left blandly homogeneous. Strictly speaking, this doesn’t constitute true replication. A cannot assemble itself from simple molecules in its environment. Its essence must come prepackaged in structure B. And the origins of structure B, unlike the origins of a gamete, lie outside of structure A.

For now, replicating nanostructures remain a fixture of theory. They lie at the horizon of the field, an Icarian undertaking for its most daring. And yet, this rudimentary yet beautiful vision of self-replication reflects a larger renaissance in DNA nanoengineering that is afoot. Each of its luminaries appears intent upon transforming nature’s blueprint into an architectural frontispiece.