Innovation and Partnerships Office

Screening to Determine the Interaction of a Protein-RNA complex 2015-121


  • Investigation of RNA-based gene expression mechanisms
  • Clinical, high-throughput screening for molecular interactions
  • Utilization of specialty antibodies and characterization of proteins


  • Faster, accurate, and sensitive method to determine protein-RNA interactions
  • Discriminates between transcribing mRNAs and long non-coding RNAs
  • Eliminates contamination issues present in currently used RNA immunoprecipitation methods that lead to false discovery


Researchers at Berkeley Lab have developed SONAR (Screening for Occupation of Nucelic Acids with target factoRs), a fast and accurate screening technology to determine if a protein of interest has the potential to interact with long non-coding RNAs (lncRNAs). This technology utilizes an enzymatic approach to label only fully formed lncRNA segments that interact with a protein of interest, while avoiding false detection signals that can come from transcribing or immature coding RNA.

Current methods to detect protein-RNA interactions involve RNA immunoprecipitation, which lacks the accuracy and purity that SONAR offers. SONAR provides an efficient, clean, and rapid way of targeting and identifying all possible protein-RNA interactions by coupling its output to Next Generation Sequencing (NGS). Aimed at increasing knowledge about the role lncRNA plays in gene expression, this method can be applied to any research that focuses on how interactions between regulatory factors and the world of non-coding RNA impact gene expression.

Furthermore, once protein-RNA interactions are identified, SONAR can be beneficial in a clinical/diagnostic setting because it determines if lncRNAs used a markers for disease are binding to their target proteins, as required to trigger cell state change. If used in a 384-well plate format, one plate reader and one technician can screen protein-RNA interactions in ~1150 patient samples in a single day.

STATUS: Available for licensing or collaborative research.