Available Technologies

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Optical probes for real-time nucleic acid detection and gene expression analysis in living cells

Fluorescent ratiometric bimolecular beacons with spatiotemporal resolution


Common gene expression analysis methods, including polymerase chain reaction, microarrays, and in situ hybridization rely on fixed or lysed cells, hindering their ability to provide spatiotemporal information. This led to the development of optical probes that enable the imaging of RNA in living cells, but most suffer from high levels of false-positive signals, due to non-specific interactions, nuclease-mediated degradation, and sequestration into the nucleus. 


Scientists in the Tsourkas Lab have designed a nucleic acid-based optical probe that, upon RNA hybridization, is capable of accurately detecting nucleic acids in living cells with high signal-to-background and little to no false-positive signals. Moreover, this ratiometric bimolecular beacon (RBMB) simultaneously measures endogenous mRNA and the efficiency of probe entry, removing cell-to-cell variability and allowing confident analysis of gene expression in individual cells.

These functional improvements over existing probes simplify protocols for quantifying gene expression and enhance the reliability of ratiometric measurements. The high signal-to-background of RBMBs also allows individual RNA transcripts to be imaged in single cells. 


  • Little to no false-positives
  • Probe distributes throughout cytoplasm
  • Reporter and Reference labels at a fixed 1:1 ratio for improved quantification of mRNA detection over time
  • Greater accuracy and reproducibility than previous ratiometric methods using separate reference and target probes


  • Simple, sensitive quantification of endogenous mRNA with spatiotemporal resolution in living cells
  • Diagnostic and therapeutic development screens to identify compounds that modify gene expression
  • Regulation/silencing of gene expression
  • Understand cell function and behavior underlying disease pathophysiology
  • Monitor transfection efficiency
  • Imaging/quantification of individual RNA transcripts in real-time.

 Fluorescent images of MEF/3T3 cells after microporation over a time course with molecular beacons (MBs) or ratiometric bimolecular beacons (RBMBs).  In (A), images of the RBMB reference dye, and in (B), images of reporter dye with RBMB in top row and conventional MB in bottom row.  In (C), image of HT1080 cells after microporation with RBMBs. The hybridization of multiple RBMBs to individual RNA transcripts allows each transcript to appear as a bright fluorescent spot that can be followed in real-time. 

Stage of Development: 

Prototype constructed and in vitro testing

Intellectual Property: 

UP application (US20120237451 A1)  

Reference Media: 

Desired Partnerships: 

  • License
  • Co-development

Patent Information:


Docket # V5104

For Information, Contact:

Joshua Jeanson Associate Director, SEAS/SAS Licensing Group
University of Pennsylvania