Lead Inventor: Dmitry Kolpashchikov Ph.D.



Problem or Unmet Need:

Quantitative real-time PCR (qPCR) is a powerful technique that is used in both clinical and basic research laboratories. Unfortunately, this technique can also be quite expensive. Traditional qPCR relies on an oligonucleotide probe specific for the template being amplified. Although qPCR primers are typically inexpensive, the fluorescent probes are not, and because the probes are sequence-specific each template must have its own probes. In addition, because of their length, probes can be relatively insensitive to single nucleotide changes in the template DNA. In order to fully realize the potential of qPCR, less expensive, more specific methods are required.



Details of the Invention:

The invention includes binary oligonucleotide probes containing both analyte binding arms and molecular beacon (MB) binding arms. The analyte binding arms are specific for the template the probe will hybridize to, and the MB binding arms specific for any one of a number of molecular beacons. Typically, these MBs may contain a fluorophore and a fluorescence-masking quencher linked to an oligonucleotide keeping them in close proximity. In this way, the binary probes' analyte binding arms can bind to the template being assayed for while their MB binding arms bind the reporter molecule. This will distance the fluorophore from its quencher and allow for the measurement of fluorescence.




Mechanism by which a binary probe can bind to a DNA analyte and induce fluorescence:







Applications:

• Clinical applications of qPCR

o Measurement of gene expression associated with diseases

• Basic research applications of qPCR

• Quantitative detection and measurement of single nucleotide polymorphisms





Advantages:

• The binary oligonucleotide probes are inexpensive to manufacture

• Analyte binding arms can be varied while keeping the MB binding arms constant

o This allows the same MBs to be used for multiple analytes

o Economy of scale: purchasing MBs will be less expensive because they can be ordered in bulk

• Each analyte binding arm is significantly shorter than the fluorescent probes currently being used for qPCR

o Specificity of binding is much higher with this invention, allowing for detection of single nucleotide polymorphisms in a template





Patent Status: Patent Pending (US20090176318A1; WO/2007/115242; EP2013561-A2) ~ see links below.



Licensing Status: Available for Licensing and Sponsored Research Support



Publications: Kolpashchikov DM., "A Binary DNA Probe for Highly Specific Nucleic Acid Recognition"; J Am Chem Soc. 2006; 128(32): 10625-10628.




Other Links:

• USPTO - US20090176318A1
• WIPO - WO/2007/115242

Further Information
Peter Golikov
Email: TechTransfer@columbia.edu

File Number: 1953