For billions of years, Nature has used DNA as a molecular bank vault; a place to store her most coveted secrets: the design blueprints essential to life.

Now, researchers at ASU's Biodesign Institute are exploring the unique information-carrying capacities of DNA, hoping to produce microscopic forms whose ability to encrypt, store and retrieve information rival those of the silicon-based semiconductor memories found in most computers.

If successful, DNA-based storage technologies could one day encode everything from a late quartet of Beethoven to a season of Westworld. The information can be imprinted in digital form in sequence strands of DNA capable of joining together with other DNA segments and self-assembling into a desired target structure, through the base-pairing properties of DNA's four nucleotides.

The technique of DNA origami permits the construction of arbitrary nanostructures in a two-step process. A long segment of single-stranded DNA, whose sequence has been designed to fold into a desired nanostructure through base-pairing, is produced. This is known as the scaffold strand. Step 2 involves the addition of shorter staple strands, which guide the folding and hold the resulting nanostructure together. The method allows the construction of a virtually endless array of forms.

Molecular cryptography with DNA origami nanostructures involves digitally encoding desired information as spot patterns within DNA strands. The encrypted data held in these information strands can subsequently be recovered when complimentary staple strands induce the DNA structure to spontaneously fold into a pre-determined pattern. Hence, the staple strands act like encryption keys. Without them, the information can not be retrieved.

The enormous variability in terms of sequence length and binding location of the staple strands used for message deciphering allows for exceptionally powerful molecular cryptography, resistant to code-breaking. Indeed, fully exploiting the encryption potential of DNA origami would permit an encryption key size of ~1500 bits, a five-fold improvement over the existing Advanced Encryption Standard (AES). {module INSIDE STORY}

The National Science Foundation has recently approved $1.5 million toward the ambitious project, which will leverage the skills of a diverse collection of scientists including researchers in chemistry, biology, physics, materials science, and engineering.

Hao Yan, director of the Biodesign Center for Molecular Design and Biomimetics and a leading figure in the field of structural DNA nanotechnology, is the Principal Investigator of the new project: "It is a truly interdisciplinary pursuit. The project combines chemistry, optics, solid-state physics, electronics, and machine learning," Yan said. (Yan is also the Milton D. Glick Distinguished Professor at ASU and researcher in the School of Molecular Sciences.)

Two notable hurdles exist to the realization of DNA information storage technologies, each of which is addressed in the new project. First, the readout for conventional DNA-based memories has had to rely on expensive, cumbersome, and error-prone methods of DNA sequencing. For the encrypted nanostructures, sapphire-based nanopores will enable rapid readout of the ultrafine nanoscopic patterns on the DNA structures, which is critical to high-security encryption, maximizing temporal readout resolution while minimizing readout noise and resultant errors.

This advance is accomplished by replacing silicon, conventionally used as a basic material in device construction but conductive and prone to high noise, with sapphire, an insulating crystal with low-noise performance. Additionally, this type of nanopore readout has the potential to be deployed as a portable device, similar to a USB dongle, and directly plugged into a computer for decoding into CDs, movies, etc.

The second major obstacle involves the accurate characterization of the resulting DNA nanostructures. This will be accomplished using a method known as DNA-PAINT, a state-of-the-art super-resolution microscopy technique that allows researchers to observe the minute DNA nanoforms well below the classic diffraction limit of light. This advance will improve the encryption throughput by a few orders of magnitude when compared with previously used atomic force microscopy.

In addition to Yan, the project includes co-PIs Rizal Hariadi and Chao Wang. All PIs are members of the Biodesign Center for Molecular Design and Biomimetics at ASU. Co-PI Hariadi is also affiliated with the Department of Physics. Co-PI Wang is from the School of Electrical, Computer & Energy Engineering.

The embryo of an animal first looks like a hollow sphere. Invaginations then appear at different stages of development, which will give rise to the body’s structures (the brain, digestive tract, etc.). According to a hypothesis that dates back more than a century, buckling could be the dominant mechanism that triggers invagination – buckling being a term that describes the lateral deformation of a material under compression. Although this explanation has long won the support of biologists, it has never been subjected to formal proof, mainly because of the difficulty – if not the impossibility – of measuring the tiny forces involved. This gap has finally been filled thanks to a study carried out by a multidisciplinary team of scientists from the University of Geneva (UNIGE). This tour de force, published in the journal Developmental Cell, owes its success to a long collaboration between specialists in biological experimentation, analytical theoretical physics, and supercomputer simulation.

“The basic question underpinning our work is to find out how to shape cellular tissue,” begins Aurélien Roux, a professor in the Department of Biochemistry in UNIGE’s Faculty of Science. Observing embryo development has made it possible to describe several mechanisms that are at work. One of these is apical constriction: a local curvature of the surface of the embryo under the effect of a coordinated deformation of the cells themselves (their “apex” tightens and their “base” relaxes). But, as Professor Roux continues: “This mechanism is by no means powerful enough to explain the appearance of major invaginations during the development of the blastocyst (one of the early stages of the embryo).” 

A century ago, biologists suggested that buckling is the physical mechanism that generates these deep folds. The same phenomenon is observed when you flatten a sheet of paper and bring the two opposite edges together: the middle of the sheet rises. In the case of embryos, the lateral force comes from cells that, when they proliferate, exert increasing pressure on the surface. Moreover, this surface is confined in a vitelline envelope, which – although it is elastic – prevents any spatial expansion.

Since the description of the phenomenon is quite eloquent and the analogies in nature are legion, the explanation easily won consensus in the biologist community. It has long been unthinkable to measure the forces present on the surface of embryos in order to verify that it really is a question of buckling (which obeys the well-known laws of material physics) and not another mechanism. 

Analytical, IT, and biological approaches

Nevertheless, the Geneva scientists – keen to provide quantitative proof of the phenomenon – conducted a long-term study. Anastasiya Trushko, a researcher in the Department of Biochemistry, and Professor Roux managed to manufacture small envelopes with all the physical properties of the natural vitelline. They also succeeded in growing a monolayer formed of a hundred cells on the inner surface. These small models, less than half a millimeter in diameter, were perfectly controlled under laboratory conditions and were used to recreate the phenomenon of invagination in vitro and to study it under a microscope. The forces involved were determined in particular thanks to small variations in the thickness of the envelope of the artificial embryos.

Meanwhile, Carles Blanch-Mercader and Karsten Kruse, respectively a researcher and professor in UNIGE’s Departments of Biochemistry and Theoretical Physics, used the measurements to show that the relationship between the strength and shape of the artificial embryos was as expected for buckling. With the help of material physics equations, they were able to extract the macroscopic mechanical parameters from the cellular tissues, such as their stiffness.

Finally, in order to link these macroscopic characteristics to biological processes at the cellular level, Aziza Merzouki and Bastien Chopard – respectively a researcher and professor in the Computer Science Department at UNIGE – simulated the development of the embryo by computer, viewing it as a set of independent cells. “The IT approach gives the unique possibility of observing certain aspects of the phenomenon that are normally inaccessible,” explains Bastien. “We can then follow in detail the temporal evolution of the buckling and, above all, understand how the biological processes (proliferation, contractility) at cell level modify the mechanical parameters of the tissue.”

Repeated round trips

There were endless round trips between the three researchers and their teams to determine the correct values for the numerous parameters that come into play and so that the three approaches arrived at the same result, i.e. as close as possible to reality. It took six years of painstaking work to get there.

“By quantifying buckling as precisely as possible, we were able to demonstrate that it is a potential mechanism for explaining the formation of invagination in embryos,” concludes Professor Roux, before adding: “It is likely that other mechanisms, such as apical constriction, initiate the folding and that the buckling accentuates it before finally obtaining the expected result.”