CRISPR: Implications for materials science
The latest possibilities for editing DNA with pinpoint accuracy are transforming.
CRISPR-Cas9 is a method of genome editing that exploits a natural DNA-snipping enzyme in bacteria, called Cas9 (CRISPR-associated protein 9) to target and edit particular genes. CRISPR stands for Clustered regularly interspaced short palindromic repeats, which are segments of DNA of a particular structure found widely in bacteria and archaea (prokaryotes). In the wild, the CRISPR-Cas9 system is part of the prokaryotic immune system, which can snip out of the genome DNA acquired from foreign sources such as phages (bacterial viruses). The same molecular machinery is now being used to enable genetic material to be cut from and pasted into the genomes of other organisms, including eukaryotes such as humans. It might offer a tool for curing genetically based diseases.
DNA has become a versatile polymeric substrate for making nanotechnological structures and artificial molecular-scale machinery for computation, pattern formation, and nanoscale assembly. For several decades now, these efforts have drawn on methods developed in and for biotechnology, and similarly they are likely to find ways of exploiting the advantages of the new technique called CRISPR/Cas9 for manipulating DNA.
Devised in 2012, CRISPR/Cas9 exploits a natural DNA-snipping enzyme in bacteria, Cas9, to target and edit particular genes. The target sequence of the DNA is recognized by a matching sequence on a “guide RNA” molecule carried alongside Cas9. This enables, for example, modified forms of the respective genes to be pasted into a genome. The method, and related approaches using other enzymes of the Cas family, could potentially supply a powerful way to cure diseases caused by mutations of one or a few specific genes, such as muscular dystrophy and thalassemia. A US clinical trial to assess the safety of CRISPR/Cas9 in a form of cancer therapy that enlists the body’s immune response to fight tumors has already received approval. The discovery of the technique, for which the key contributions are generally attributed to biochemists Emmanuelle Charpentier, Jennifer Doudna, and Feng Zhang, is now widely tipped for a Nobel prize.
DNA nanotechnology and materials
Such a tool for targeting and editing DNA with high precision could be a fantastic
addition to the toolbox of the many researchers seeking to repurpose this programmable molecule for making artificial, self-assembling constructs and materials.
That vision began with the pioneering work of Nadrian Seeman of New York University, who showed in 1991 that DNA strands could be encoded with the information they need to assemble spontaneously into cube-shaped molecules. Since then, the field of DNA nanotechnology has expanded in many directions. It has been used for complicated “molecular origami,” such as boxes with lids that can be opened with a molecular trigger, and extended two-dimensional patterned arrays.
Erik Winfree and co-workers at the California Institute of Technology (Caltech) have developed a form of DNA computation in which tile-like structures are programmed to assemble like cellular automata. Several researchers have made DNA molecular machines that can change shape in a controllable and perhaps cyclic fashion. In 2006, Paul W.K. Rothemund, also at Caltech, showed how to program DNA sequences systematically so that they fold up into any arbitrary structure—an approach that can now yield intricate three-dimensional (3D) architectures. DNA has proved useful for boosting the performance of photonic devices such as organic light-emitting diodes, assembling nanoparticles, and storing data.
DNA nanotechnology is now moving from the test tube to living cells, for example
for imaging, drug delivery, and smart therapeutics. Some of this work overlaps with the uses of artificial DNA in synthetic biology, where for example some researchers imagine creating autonomous DNA machines to monitor health in the body and respond to the threat of disease. Carolyn Bertozzi and Zev Gartner of the University of California, Berkeley, have shown that DNA tags on the surfaces of living cells can be used to assemble them in a programmable way into controlled micro-tissues: “living” biomaterials, you might say.
Underpinning all of these efforts are advances in biotechnology and chemical synthesis that have made it possible to specify the precise base sequence of artificial DNA strands, so that the way they stick together through base-pairing into double helices and other structures can be predicted and directed. The CRISPR/Cas9 method makes this kind of control easier and more precise. But where exactly might that be useful for DNA nanoengineers?
One answer is that it might simply help to make the long strands needed for DNA origami. “At the moment, DNA origami relies on a natural long DNA from the M13 bacteriophage [a bacterial virus],” says biochemist Anthony Genot of LIMMS/CNR-IIS and The University of Tokyo, “because it is difficult to synthesize chemically strands longer than 100–200 nucleotides.” CRISPR could be used to splice fragments into longer strands and police the accuracy of their sequences.
CRISPR might also be used to introduce functionality into DNA origami, says Chase Biesel of North Carolina State University, who uses gene editing to engineer gut bacteria. “I can imagine CRISPR/Cas9 being used to actively modify such nucleic-acid constructs,” he says—“either by cleaving existing structures to drive large structural changes or to release an entrapped chemical.”