Friday, December 31, 2004

In vitro Gene Production... on a chip!

Traditionally, when you're interested in studying a gene or want to use it in a fancy molecular construction, you have only one option : molecular cloning techniques which are (very) time consuming. Recently, Gene production techniques emerged; they are relatively rapid (turnaround ranging from 2 weeks to a month or more, for more complicated construction) but very expensive (1.5$ / basepair... so a pricetag in the thousands is not uncommon). The technique involve oligo synthesis and stitching by PCR; it work well for small genes, but large constructions can be problematic. Researchers at the University of Michigan just invented a way to easily build genes using a microfluidics approach.

It's fast and inexpansive. And it will open loads of interesting research avenues and speed up drug development for sure!

Synthetic biology: Researchers mass produce genes on a chip

Imagine that the bricks used to build a house cost $1,000 each—building a home would be cost prohibitive. Similarly, the bricks to build living organisms—genes and genetic assemblies—can cost thousands of dollars to make in the lab, which is also cost prohibitive.

But now, scientists have developed a way to make the materials for genes on a microchip in mass quantities, for a fraction of the current cost.

The technology enabled scientists to make an important part of the genome for an E-coli bug, and to reproduce the instructions for making proteins. This has significant applications in vaccine production, gene therapy, and DNA sensors and diagnostics.

"The significance of our paper is that for the first time, we have a mechanism for us to make the genes in high accuracy, very inexpensively, and to make those genes containing the information for the protein factory in an organism" that synthesize all other proteins in the body, said Erdogan Gulari, a University of Michigan professor, the Donald L. Katz Collegiate Professor of Chemical Engineering and co-author of a paper on the topic to appear in the Dec. 23 Nature. "This is the starting point to making a complete functioning organism that can produce energy, neutralize toxins, and produce medically useful proteins, for the benefit of human health and quality of life."

The paper, entitled "Accurate multiplex gene synthesis from programmable DNA microchips," was co-authored by researchers from the U-M College of Engineering, Harvard University, University of Houston and Atactic Technologies Inc. The technology is currently licensed to Atactic, a company founded by a U-M College of Engineering alum Xiaochuan Zhou, professors Xiaolian Gao of University of Houston, and Gulari.

If made the standard way, a typical gene can cost several thousand to hundreds of thousands of dollars, Gulari said. That's because the cost of putting together each nucleotide, the building block of DNA and RNA, comes to $2 to $7 dollars each. Genes contain thousands to tens of thousands of oligonucleotides, short chains of nucleotides that join together to make genes. So synthesizing all the genes of even the most primitive living organism, which has several thousands of genes, could cost millions of dollars and take years, Gulari said.

The new method uses technology similar to that used to make computer chips, Gulari said, and generates oligonucleotides in thousands of tiny reaction wells and releases the sequences synthesized, Gulari said.

Scientists start with a thumbnail-sized silicon or glass chip containing microchannels and microwells loaded with low-cost reagent. The wells are so tiny, Gulari said, that thousands of them can be filled by half a drop of water. By shining tiny pixels of light at selected areas on the chip in a predetermined manner, scientists made thousands of gene fragments of specific sequences each containing 30-70 nucleotides. They then collected them in a solution microtube, and stitched them together in the desired order to produce the genes by enzymes.

The benefits of synthetic genes are tremendous, Gulari said.

"For instance, these products can be used to improve DNA sensor and diagnostics for comprehensive and more sensitive genetic analysis, and to produce the blueprint for novel proteins," Gulari said. "Some of these proteins would be too toxic to obtain from natural sources, so the synthetic version is much safer. Some of these man-made proteins have novel functions which do not exist in nature, which potentially can be a new generation of vaccines or therapeutics."

For instance, Gulari said, 50 percent of drug molecules are based on proteins and antibodies, and there are over 371 new products currently in clinical trials targeting more than 200 diseases. Consequently, there is great interest in creating humanized antibodies for early detection of infection and for medicines. For these applications, millions of new proteins and antibodies must be tested, he said. This technology makes that possible.

A forerunner to the synthetic gene was the birth of recombinant DNA (the joining of DNA from different species and subsequently inserting the hybrid DNA into a host cell) about 30 years ago. Recombinant DNA, Gulari said, has become an indispensable tool for advancing biochemical and biomedical sciences for improving health care and disease treatment. Without recombinant DNA technologies, there wouldn't be insulin, alpha interferon (cancer drug), a hepatitis B vaccine, and many human growth hormones and other therapeutic proteins, he said.



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