APPLICATIONS OF TECHNOLOGY:
- Translation of DNA sequences into affinity labeled proteins
- Protein isolation for downstream characterization
- For application in transcription factor (TF) binding site discovery methods (e.g., DAP-seq, SELEX), RNA protein-binding site discovery, and protein-protein interaction studies
- This method is equally effective, ~40x faster, and ~10x less expensive than current methods
- This cost and time savings, for the first time, make high-throughput pull-down feasible for laboratories and biotechnology companies
Mapping transcription factors (TFs) to their target genes is fundamental to illuminating how gene networks function. However, information regarding TF-gene interactions is lacking for most organisms. The primary technical bottleneck to acquire such information is the significant upfront investment required to clone and express the tagged TFs used in in vitro assays. To our current knowledge, this is the first use of biotin-tRNA to isolate proteins for protein interaction studies.
Researchers at Berkeley Lab have developed Biotin-DAP-seq, a streamlined clone-free workflow where tagged TF proteins are expressed from DNA templates that are polymerase chain reaction (PCR)-amplified directly from genomic DNA, cDNA or plasmids.
The new invention enables downstream affinity capture of TFs along with bound DNA sequences. It removes the time and cost associated with generating a clone for all proteins to be expressed in an in vitro expression system. The same approach used to immobilize TFs for DAP-seq could also be used for a low-cost high-throughput protein isolation for downstream characterization (i.e. RNA-protein interactions, protein-protein interactions, ligand binding, structural analysis).
Ultimately, Biotin DAP-seq obviates the need for cloning and purifying TFs for the original DAP-seq and therefore enables applications at scale to any organism of interest. For instance, current throughput allows 400 TFs per week to be processed by a single laboratory technician and is applicable to TFs from all domains of life including bacteria, archaea, and eukaryotes.
The first technology to allow high-throughput protein pull-down, Biotin DAP-seq will allow a new class of experiments in molecular biology and increase our ability to understand the genetic underpinnings of organisms, creating a new market. This technology can be used in a number of exploratory research experiments, and would be a great candidate for licensing by companies that sell research tools for biological assays.
DEVELOPMENT STAGE: Proven principle
FOR MORE INFORMATION:
- Ronan O’Malley
- Leo Baumgart
STATUS: Patent pending.
OPPORTUNITIES: Available for licensing or collaborative research.