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Chemical and Biomolecular Engineering

Researchers at the University of Illinois and the University of Massachusetts, Amherst have taken the first steps toward gaining control over the self-assembly of synthetic materials in the same way that biology forms natural polymers. This advance could prove useful in designing new bioinspired, smart materials for applications ranging from drug delivery to sensing to remediation of environmental contaminants.

Proteins, which are natural polymers, use amino acid building blocks to link together long molecular chains. The specific location of these building blocks, called monomers, within these chains creates sequences that dictate a polymer’s structure and function. In the journal Nature Communications, the researchers describe how to utilize the concept of monomer sequencing to control polymer structure and function by taking advantage of a property present in both natural and synthetic polymers – electrostatic charge.

(from left) Charles Sing, professor of theoretical and computational polymer physics; graduate student Jason Madinya; and graduate student Tyler Lytle.
Inspired by the principles of natural polymer synthesis, Illinois chemical and biomolecular engineering professor Charles Sing, left, and graduate students Jason Madinya and Tyler Lytle co-authored a study that found they could create new synthetic materials by tuning the electrostatic charge of polymer chains. Photo by L. Brian Stauffer

“Proteins encode information through a precise sequence of monomers. However, this precise control over sequence is much harder to control in synthetic polymers, so there has been a limit to the quality and amount of information that can be stored,” said Charles Sing, a professor of chemical and biomolecular engineering at Illinois and a study co-author. “Instead, we can control the charge placement along the synthetic polymer chains to drive self-assembly processes.”

Sarah Perry, a study co-author and professor of chemical engineering at the University of Massachusetts, Amherst. She also is a Chemical Engineering alumnus (PhD ’10, Kenis) of Illinois.

“Our study focuses on a class of polymers, called coacervates, that separate like oil and water and form a gel-like substance,” said Sarah Perry, a study co-author and University of Massachusetts, Amherst chemical engineering professor, as well as an Illinois alumna. She received her PhD in 2010, advised by Dr. Paul Kenis.

Through a series of experiments and computer simulations, the researchers found that the properties of the resulting charged gels can be tuned by changing the sequence of charges along the polymer chain.

“Manufacturers commonly use coacervates in cosmetics and food products to encapsulate flavors and additives, and as a way of controlling the ‘feel’ of the product,” Sing said. “The challenge has been if they need to change the texture or the thickness, they would have to change the material being used.”

Sing and Perry demonstrate that they can rearrange the structure of the polymer chains by tuning their charge to engineer the desired properties. “This is how biology makes the endless diversity of life with only a small number of molecular building blocks,” Perry said. “We envision bringing this bioinspiration concept full circle by using coacervates in biomedical and environmental applications.”

The results of this research open a tremendous number of opportunities to expand the diversity of polymers used and the scale of applications, the researchers said. “Currently, we are working with materials on the macro scale – things that we can see and touch,” Sing said. “We hope to expand this concept into the realm of nanotechnology, as well.”

The National Science Foundation and the U. of I. Graduate College supported this research.

Written by Lois Yoksoulian, Physical Sciences Editor, University of Illinois News Bureau

To reach Charles Sing, call 217-244-6671; cesing@illinois.edu.

To reach Sarah Perry, call 413-545-6252; perrys@engin.umass.edu.

The paper “Sequence and entropy-based control of complex coacervates” is available online and from the U. of I. News Bureau. DOI: 10.1038/s41467-017-01249-1

When it comes to efficiency, sometimes it helps to look to Mother Nature for advice – even in technology as advanced as printable, flexible electronics.

Researchers at the University of Illinois have developed bio-inspired dynamic templates used to manufacture organic semiconductor materials that produce printable electronics. It uses a process similar to biomineralization – the way that bones and teeth form. This technique is also eco-friendly compared with how conventional electronics are made, which gives the researchers the chance to return the favor to nature.

from bottom right, clockwise: Ying Diao, professor of chemical and bimolecular engineering; Diwakar Shukla, professor of chemical and bimolecular engineering; Chuankai Zhao, graduate student; and Erfan Mohammadi, graduate student.
Illinois researchers have developed a new dynamic template that could be critical to the advancement of printable electronics technology. From bottom right, clockwise: Ying Diao, professor of chemical and biomolecular engineering; Diwakar Shukla, professor of chemical and biomolecular engineering; Chuankai Zhao, graduate student; and Erfan Mohammadi, graduate student.

Templating is used for making near-perfect semiconductors to enhance their electronic properties, or to modulate the spacing between atoms for better electronic properties. These templates help to properly align the atoms of semiconductor materials, typically silicon or germanium, into the form that is needed.

However, this conventional methodology only works well for rigid nanoelectronic devices. The larger, more disordered organic polymer molecules needed to make flexible electronics cannot arrange around a fixed template.

In a new report in the journal Nature Communications, chemical and biomolecular engineering professor Ying Diao, graduate student Erfan Mohammadi and co-authors describe how the biomineralization-like technique works.

In nature, some biological organisms build mineralized structures by harvesting or recruiting inorganic ions using flexible biologic polymers. Similarly, the templates Diao’s group developed are made up of ions that reconfigure themselves around the atomic structure of the semiconductor polymers. This way, the large polymer molecules can form highly ordered, templated structure, Diao said.

This highly ordered structure overcomes the quality control issues that have plagued organic semiconductors, slowing development of flexible devices.

“Our templates allow us to control the assembly of these polymers by encouraging them to arrange on a molecular level. Unlike printing of newspapers, where the ordering of the ink molecules does not matter, it is critical in electronics,” Diao said.

The manufacturing process that can use these dynamic templates is also eco-friendly. Unlike conventional semiconductor manufacturing methods, which require temperatures of about 3,000 degrees Fahrenheit and produce a significant amount of organic waste, this process produces little waste and can be done at room temperature, cutting energy costs, Diao said.

“Our research looks to nature for solutions,” Diao said. “In nature, polymers are used to template ions, and we did the opposite – we use ions to template polymers to produce flexible, lightweight, biointegrated electronics at low cost and large scale.”

Other co-authors of this work include graduate student Ge Qu and postdoctoral scholar Fengjiao Zhang of chemical and biomolecular engineering; professor Jian-Min Zuo and graduate student Yifei Meng of materials science and engineering; and professor Jianguo Mei and graduate student Xikang Zhao of Purdue University.

The U. of I., the National Science Foundation, the United States Department of Energy and the Office of Naval Research Young Investigator Program supported this research.

By Lois Yoksoulian, Physical Sciences Editor, University of Illinois News Bureau; 217-244-2788; leyok@illinois.edu

To reach Ying Diao, call 217-300-3505; yingdiao@illinois.edu.

The paper “Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films” is available from the U. of I. News Bureau.

New approach combines synthetic biology, genome editing tools, and automation to quickly and effectively produce novel yeast strains

One of humankind’s oldest industrial partners is yeast, a familiar microbe that enabled early societies to brew beer and leaven bread and empowers modern ones to synthesize biofuels and conduct key biomedical research. Yeast remains a vital biological agent, yet our ability to explore and influence its genomic activity has lagged.

In a new article in Nature Communications (DOI: 10.1038/NCOMMS15187), University of Illinois researchers describe how their successful integration of several cutting-edge technologies—creation of standardized genetic components, implementation of customizable genome editing tools, and large-scale automation of molecular biology laboratory tasks—will enhance our ability to work with yeast. The results of their new method demonstrate its potential to produce valuable novel strains of yeast for industrial use, as well as to reveal a more sophisticated understanding of the yeast genome.

Zhao and Si
Dr. Huimin Zhao and IGB Research Fellow Tong Si

“The goal of the work was really to develop a genome-scale engineering tool for yeast . . . traditional metabolic engineering focused on just a few genes and the few existing genome-scale engineering tools are only applicable to bacteria, not eukaryotic organisms like yeast,” said Steven L. Miller Chair of Chemical and Biomolecular Engineering Huimin Zhao, who led the study. “A second innovation is the use of synthetic biology concepts, the modularization of the parts, and integration with a robotic system, so we can do it in high-throughput.”

The team focused on yeast in part because of its important modern-day applications; yeasts are used to convert the sugars of biomass feedstocks into biofuels such as ethanol and industrial chemicals such as lactic acid, or to break down organic pollutants. Because yeast and other fungi, like humans, are eukaryotes, organisms with a compartmentalized cellular structure and complex mechanisms for control of their gene activity, study of yeast genome function is also a key component of biomedical research.

“In basic science, a lot of fundamental eukaryotic biology is studied in yeast,” said Tong Si, a Carl R. Woese Institute for Genomic Biology Research Fellow. “People have a limited understanding of these complicated systems. Although there are approximately 6,000 genes in yeast, people probably know less than 1,000 by their functions; all the others, people do not know.”

The group took the first step toward their goal of a novel engineering strategy for yeast by creating what is known as a cDNA library: a collection of over 90% of the genes from the genome of baker’s yeast (Saccharomyces cerevisiae), arranged within a custom segment of DNA so that each gene will be, in one version, overactive within a yeast cell, and in a second version, reduced in activity.

Zhao and colleagues examined the ability of the CRISPR-Cas system, a set of molecules borrowed from a form of immune system in bacteria (CRISPR stands for clustered regularly interspaced short palindromic repeats, describing a feature of this system in bacterial genomes). This system allowed Zhao to make precise cuts in the yeast genome, into which the standardized genetic parts from their library could insert themselves.

“The first time we did this, in 2013, there was no CRISPR . . . the best we could get was 1% of the cells modified in one run,” said Si. “We struggled a little on that, and when CRISPR came out, that worked. We got it to 70% [cells modified], so that was very important.”

With gene activity-modulating parts integrating into the genome with such high efficiency, the researchers were able to randomly generate many different strains of yeast, each with its own unique set of modifications. These strains were subjected to artificial selection processes to identify those that had desirable traits, such as the ability to survive exposure to reagents used in the biofuel production process.

This selection process was greatly aided by the Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB), a robotic system that performs most of the laboratory work described above in an automated way, including selection of promising yeast strains. Use of iBioFAB greatly accelerated the work, enabling simultaneous creation and testing of many unique strains. The iBioFAB was conceived and developed by the Biosystems Design research theme at the Carl R. Woese Institute for Genomic Biology (IGB), which is led by Zhao.

With support from the High Performance Biological Computing Group at Illinois, Zhao, Si and their colleagues analyzed the modified genomes of their most promising yeast strains.  They identified combinations of genes whose altered activities contributed to desirable traits; the functions of some of these genes were previously unknown, demonstrating the technique’s ability to generate new biological knowledge.

“I think the key difference between this method and the other existing metabolic engineering strategies in yeast is really the scale,” said Zhao. “The current metabolic engineering strategies are all focused on just a few genes, dozens of genes at most . . .  it’s very intuitive.  With this we can explore all the genes, we can identify a lot of targets that cannot be intuited.”

The work, which was funded by the Roy J. Carver Charitable Trust, IGB, Defense Advanced Research Program Agency, and National Academies Keck Futures Initiative on Synthetic Biology, paves the way for similar approaches to broad-scale, automated genome engineering of other eukaryotic species.

By Claudia Lutz, Carl R. Woese Institute for Genomic Biology

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