New method generates unlimited, high-quality antibodies for genetics research

August 26, 2013

Modern genomic studies rely on precise and sophisticated technology, but the antibodies used to identify proteins that control gene expression can be unreliable as a research tool, placing time, money and study results at risk. Now, scientists from the University of Chicago have devised a novel method for creating high-quality, specific and reproducible antibodies that eliminate an "antibody bottleneck" that has plagued genomics research.

While the sequence of DNA serves as the blueprint for life, the regulation of that genetic code relies on a variety of critical mechanisms, collectively called epigenetics. Among the most important are histones, proteins that act as spools around which DNA winds. Subtle chemical modifications to histones play an essential role in turning genes on or off and are an important target for genetic research. Antibodies, short segments of protein that bind to these modifications, are the primary tool used by scientists to identify the effect of histones on gene regulation.

However, as antibodies are generated from animals, the variations in quality and efficacy between batches can be great. Considerable time and effort have to be spent on testing new antibody lots, and unpredictable differences can make it hard to compare results between groups and, over time, prevent progress in the field.

To address this "antibody bottleneck," Shohei Koide, PhD, professor of biochemistry and molecular biophysics at the University of Chicago, and his team harnessed the power of directed evolution, a method that mimics natural selection and protein design. They first created a large catalog of bacteria that were programmed with artificially synthesized, recombinant DNA to produce different antibodies. After isolating a single antibody that appeared promising in recognizing histone modification, the team analyzed its structure in detail to look for possible improvements. Based on this analysis, they created another set of recombinant DNA, programmed bacteria with it and looked for a new, improved antibody.

They repeated this iterative process of analysis and improvement until they created a sequence of recombinant DNA that produced a highly reliable, reproducible and specific antibody suitable for histone modification research.

"For the first time, we've demonstrated that high-quality histone modification antibodies can be generated through recombinant techniques. We can produce the same antibody over and over again, in large quantities, with no change in quality," Koide said. "We believe our antibodies will replace conventional antibodies in standard research applications and enable new methods."

The team is applying this method toward generating antibodies that can be used to recognize other regulatory proteins and transcription factors important to genetic research. They also are exploring the utility of their antibodies in clinical applications. Koide and his collaborators are developing tests to identify genetic abnormalities in diseases and recently received funding from the Facioscapulohumeral Muscular Dystrophy Society to pursue research in this area.

"Variation of antibody quality was a fundamental roadblock for establishing clinical tests that look at abnormalities in chromatin modifications. Clearly, in order for such a test to be reliable, antibody properties must remain constant. We will be able to make fundamental contributions to realizing such methods," Koide said.

The work was published Aug. 18 in Nature Methods.

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