DNA-Encoded Antibody Libraries Enable Multiplexed Analysis of Complex Biological Samples

During the past several years, breakthroughs in genomic and proteomic technologies have enabled researchers to more clearly identify the biochemical networks that malfunction when a healthy cell becomes malignant. Now, James Health, Ph.D., and colleagues at the California Institute of Technology have developed a new approach to genomic and proteomic analysis, one that detects messenger RNA (mRNA), proteins, and even whole cells simultaneously on a single glass slide.

This new method, described in the Journal of the American Chemical Society, stands to simplify efforts to combine genomic and proteomic analyses in the same experiment. Heath is a co-principal investigator of the Nanosystems Biology Cancer Center (NSBCC) CCNE.

Current technologies for capturing proteins and cells for further analysis rely on antibodies that recognize and bind strongly to specific proteins, while gene analysis methods utilize complementary DNA probes as capture agents. In both instances, the capture probes can be attached to a glass slide, forming either a protein-detection or gene-detection array.

Because of the unique biochemical characteristics of antibodies and DNA probes, putting both types of capture probes on the same slide is not possible. Heath and his colleagues overcame this problem by first adding a unique DNA tail to each antibody capture probe, and then using a traditional DNA-based array to capture both the antibodies – using their DNA tails – and mRNAs of interest in a biological sample.

To analyze the proteins and nucleic acids in a biological sample, a library of DNA-coded antibodies is mixed with the sample and incubated for two hours in order to give the antibodies sufficient time to find and bind to their specific targets. The mixture is then applied to a DNA array. Each spot of DNA on the array binds to either one particular antibody-DNA combination or one specific mRNA segment. After a suitable incubation period, the array is then analyzed using a fluorescence microscope. The investigators note that they are now adapting their technology for use in a high-throughput microfluidic-based device.

This work, which was supported by the National Cancer Institute’s Alliance for Nanotechnology in Cancer, is detailed in a paper titled, “DNA-encoded antibody libraries: A unified platform for multiplexed cell sorting and detection of genes and proteins.” Investigators from the University of California, Los Angeles, also participated in this study. This paper was published online in advance of print publication. An abstract is available at the journal’s website. View abstract.


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