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Manufacturing of Smart multifunctional materials employing Synthetic Biology and DNA

“Smart” materials are an emerging category of multifunctional materials with physical or chemical properties that can be controllably altered in response to an external stimulus. By combining the standard properties of the advanced material with the unique ability to recognize and adapt in response to a change in their environment, these materials are finding applications in areas such as sensing and drug delivery.

 

 

However, developing Smart materials and products have many challenges like novel fabrication techniques (e.g. dispersion, alignment); in-process metrology; material characterization and in-situ monitoring; yield optimization; accelerated life tests to determine material durability and techniques to advance disassembly and recovery at end of life.

 

Now scientists have turned to Synthetic biology or DNA for manufacturing of smart multifunctional materials. Synthetic biology can be defined as engineering approach to biology. And it aims to re-design of natural biological systems for useful purposes as well as design and construction of new biological parts, devices, and systems.

 

How it does it? Any organism’s sensing, metabolic, and decision-making capabilities depend on unique sequence of DNA bases within their genome. These DNA base pair sequences determine how a cell grows and what goes on inside it or what it produces. By changing an organism’s genome sequence, we can alter these cellular functions, and thereby engineer them.

 

Let’s now consider some of the technologies and tools of synthetic biology which allow us to engineer biological systems. The first technology is to read DNA or DNA Sequencing, that determines the order of the DNA base pairs or biological instructions that are contained in a strand of DNA.

 

A difference from the expected sequence of a gene is called a variant or mutation. Comparing healthy and mutated DNA sequences scientists can diagnose different diseases including cancers and deliver more individualized medical care. The rapid speed of modern DNA sequencing technology has enabled sequencing of complete genomes of numerous types and species of life, including microbes, animals, plants, and the human genome.

 

The second is gene editing technology, and CRISPR has become one of the most popular gene editing tools as it is fast, cheap, and easy to use. It can locate, cut, and replace DNA sequences at specific locations modifying the function of that gene. CRISPR uses modified RNA sequence to recognize DNA sequence in genome and bind to it.  The RNA also binds to the Cas9 enzyme that cuts the DNA at the targeted location. CRISPR enables Gene therapy that add, delete, or correct genetic material to treat a disease.

 

Next technology is DNA synthesis that is the natural or artificial creation of DNA molecules. We have already seen natural creation, during cell division DNA helix splits itself and each strand of DNA serve as a pattern for duplicating the sequence of bases. This is natural DNA synthesis process is called DNA replication as it self-replicates or make copies of itself.

 

Traditionally Artificial DNA synthesis techniques were chemical and relied on toxic chemicals and generated hazardous waste. Further it could synthesize short DNA or RNA molecules called oligonucleotides about 200 bases long. Lengthy sequences resulted in more errors and low yield of correct sequences. To assemble even a small gene, scientists used to synthesize it in short segments and then stitch them together. This was also prone to failure and often required multiple attempts. Therefore, traditional DNA synthesis particularly in long strands, was slower and expensive.

 

New DNA synthesis technique is called Enzymatic DNA synthesis (EDS). This technique employs DNA-synthesizing enzyme found in cells of the immune system. This enzyme can naturally add nucleotides to an existing DNA molecule in water, where DNA is most stable. The improved precision of this technique allow synthesis of DNA strands several thousand bases long or size of a medium-sized gene.

 

This technology has enabled development of DNA printers. Earlier scientists would search out sections of DNA code in nature, cut the DNA out of existing organisms, and then insert it into a new host organism in a ‘cut-and paste’ process. DNA printers can build artificial DNA from scratch with any DNA code you want. You don’t need to find DNA in nature anymore, you just buy it in from the internet. There are also several commercial companies that provide DNA synthesis services.

 

Most synthetic biology companies are coming up with artificial DNA codes that can be inserted into microbes, plants or animals forcing them to make industrially useful compounds. The self-replicating property of DNA allow this to be scaled up, to millions of  ‘programmed cell factories’ filling a big industrial vat.

 

In effect Synthetic biology has turned the bioscience into the future manufacturing paradigm where Companies can engineer and manufacture an infinite quantity of things, cell by cell, from scratch. These bioengineered microorganisms, plants and animals can produce pharmaceuticals, repair defective genes, develop new generations of vaccines, destroy cancer cells, detect toxic chemicals, break down pollutants, and generate hydrogen for the post petroleum economy.

 

Deoxyribonucleic acid (all-DNA and DNA-hybrid) materials have been used extensively to produce soft materials (hydrogels) of unique properties. DNA hydrogels respond to certain physicochemical triggers (pH, temperature, light, magnetic field, metal ions, chemical compounds, enzymes, other biomolecules) and undergo reversible-switchable phase transitions finding their scope in the fields of biosensing and 3D cell imaging, drug delivery, cell cultures and tissue engineering, immune-modulation, cell-free protein synthesis, intelligent materials, environmental protection, and nano-biomaterials.

Making 3-D nanosuperconductors with DNA

Three-dimensional (3-D) nanostructured materials—those with complex shapes at a size scale of billionths of a meter—that can conduct electricity without resistance could be used in a range of quantum devices. For example, such 3-D superconducting nanostructures could find application in signal amplifiers to enhance the speed and accuracy of quantum computers and ultrasensitive magnetic field sensors for medical imaging and subsurface geology mapping. However, traditional fabrication tools such as lithography have been limited to 1-D and 2-D nanostructures like superconducting wires and thin films.

 

In Nov 2020, S cientists from the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory, Columbia University, and Bar-Ilan University in Israel reported have developed a platform for making 3-D superconducting nano-architectures with a prescribed organization. As reported in the Nov. 10 issue of Nature Communications, this platform is based on the self-assembly of DNA into desired 3-D shapes at the nanoscale. In DNA self-assembly, a single long strand of DNA is folded by shorter complementary “staple” strands at specific locations—similar to origami, the Japanese art of paper folding.

 

“Because of its structural programmability, DNA can provide an assembly platform for building designed nanostructures,” said co-corresponding author Oleg Gang, leader of the Soft and Bio Nanomaterials Group at Brookhaven Lab’s Center for Functional Nanomaterials (CFN) and a professor of chemical engineering and of applied physics and materials science at Columbia Engineering. “However, the fragility of DNA makes it seem unsuitable for functional device fabrication and nanomanufacturing that requires inorganic materials. In this study, we showed how DNA can serve as a scaffold for building 3-D nanoscale architectures that can be fully “converted” into inorganic materials like superconductors.”

 

To make the scaffold, the Brookhaven and Columbia Engineering scientists first designed octahedral-shaped DNA origami “frames.” Aaron Michelson, Gang’s graduate student, applied a DNA-programmable strategy so that these frames would assemble into desired lattices. Then, he used a chemistry technique to coat the DNA lattices with silicon dioxide (silica), solidifying the originally soft constructions, which required a liquid environment to preserve their structure. The team tailored the fabrication process so the structures were true to their design, as confirmed by imaging at the CFN Electron Microscopy Facility and small-angle X-ray scattering at the Complex Materials Scattering beamline of Brookhaven’s National Synchrotron Light Source II (NSLS-II). These experiments demonstrated that the structural integrity was preserved after they coated the DNA lattices.

 

“In its original form, DNA is completely unusable for processing with conventional nanotechnology methods,” said Gang. “But once we coat the DNA with silica, we have a mechanically robust 3-D architecture that we can deposit inorganic materials on using these methods. This is analogous to traditional nanomanufacturing, in which valuable materials are deposited onto flat substrates, typically silicon, to add functionality.” The team shipped the silica-coated DNA lattices from the CFN to Bar-Ilan’s Institute of Superconductivity, which is headed by Yosi Yeshurun. Gang and Yeshurun became acquainted a couple years ago, when Gang delivered a seminar on his DNA assembly research. Yeshurun—who over the past decade has been studying the properties of superconductivity at the nanoscale—thought that Gang’s DNA-based approach could provide a solution to a problem he was trying to solve: How can we fabricate superconducting nanoscale structures in three dimensions?

 

“Previously, making 3-D nanosuperconductors involved a very elaborate and difficult process using conventional fabrication techniques,” said Yeshurun, co-corresponding author. “Here, we found a relatively simple way using Oleg’s DNA structures.” At the Institute of Superconductivity, Yeshurun’s graduate student Lior Shani evaporated a low-temperature superconductor (niobium) onto a silicon chip containing a small sample of the lattices. The evaporation rate and silicon substrate temperature had to be carefully controlled so that niobium coated the sample but did not penetrate all the way through. If that happened, a short could occur between the electrodes used for the electronic transport measurements. “We cut a special channel in the substrate to ensure that the current would only go through the sample itself,” explained Yeshurun.

 

The measurements revealed a 3-D array of Josephson junctions, or thin nonsuperconducting barriers through which superconducting current tunnels. Arrays of Josephson junctions are key to leveraging quantum phenomena in practical technologies, such as superconducting quantum interference devices for magnetic field sensing. In 3-D, more junctions can be packed into a small volume, increasing device power.

 

“DNA origami has been producing beautiful and ornate 3-D nanoscale structures for almost 15 years, but DNA itself is not necessarily a useful functional material,” said Evan Runnerstrom, program manager for materials design at the U.S. Army Combat Capabilities Development Command Army Research Laboratory of the U.S. Army Research Office, which funded the work in part. “What Prof. Gang has shown here is that you can leverage DNA origami as a template to create useful 3-D nanostructures of functional materials, like superconducting niobium. This ability to arbitrarily design and fabricate complex 3-D-structured functional materials from the bottom-up will accelerate the Army’s modernization efforts in areas like sensing, optics, and quantum computing.”

 

“We demonstrated a pathway for how complex DNA organizations can be used to create highly nanostructured 3-D superconducting materials,” said Gang. “This material conversion pathway gives us an ability to make a variety of systems with interesting properties—not only superconductivity but also other electronic, mechanical, optical, and catalytic properties. We can envision it as a “molecular lithography,” where the power of DNA programmability is transferred to 3-D inorganic nanofabrication.”

 

CRISPR  gene-editing tool used to trigger smart materials that can deliver drugs and sense biological signals.

Scientists have wielded the gene-editing tool CRISPER to make scores of genetically modified organisms, as well as to track animal development, detect diseases and control pests. Now, they have found yet another application for it: using CRISPR to create smart materials that change their form on command.

 

The shape-shifting materials could be used to deliver drugs, and to create sentinels for almost any biological signal, researchers report in Science in August 2019. The study was led by James Collins, a bioengineer at the Massachusetts Institute of Technology in Cambridge.

 

Collins’ team worked with water-filled polymers that are held together by strands of DNA, known as DNA hydrogels. Materials called hydrogels are made of water-filled polymers. Collins and his team turned to a form of CRISPR that uses a DNA-snipping enzyme called Cas12a. (The gene-editor CRISPR–Cas9 uses the Cas9 enzyme to snip a DNA sequence at the desired point.) The Cas12a enzyme can be programmed to recognize a specific DNA sequence. The enzyme cuts its target DNA strand, then severs single strands of DNA nearby.

 

This property allowed the researchers to build a series of CRISPR-controlled hydrogels containing a target DNA sequence and single strands of DNA, which break up after Cas12a recognizes the target sequence in a stimulus. The break-up of the single DNA strands triggers the hydrogels to change shape or, in some cases, completely dissolve, releasing a payload (see ‘CRISPR-controlled gels’).

 

The team created hydrogels programmed to release enzymes, small molecules and even human cells — which could be part of a therapy — in response to stimuli. Collins hopes that the gels could be used to make smart therapeutics that release, for example, cancer drugs in the presence of a tumour, or antibiotics around an infection

 

 

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