Lead Inventor: Dmitry Kolpashchikov Ph.D.


Tech Ventures Reference: IR 1941 & 1953



Problem or Unmet Need:

Sequence specific detection of nucleic acids is crucial to genome study, disease diagnosis, mRNA monitoring in living cells. Fluorescent analysis of nucleic acid offers easy and instant detection of specific genomic sequence through visible fluorescent response after hybridization of the probe to complementary nucleic acids. However, it is limited by selectivity and efficacy under physiological conditions. In addition, current approaches for DNA and RNA analysis rely on the ability of the probe to recognize specific sequence by forming hybrid duplexes. However, the long nucleotide hybrid duplex is not sensitive to single nucleotide mismatches at mild or physiological conditions, which limit its use. Therefore there is need for an easy and reliable method to detect single nucleic acid mismatches.



Details of the Invention:

This invention is directed to binary nucleic analysis, which probes can be made of DNA or RNA that recognize nucleic acid analytes (both DNA and RNA) and detect single nucleotide mismatches without PCR amplification. One group of binary probes comprises a) a molecular beacon binding arm complementary to and selectively hybridizes with molecular beacon. b) a linker that is flanked by oligonucleotide analyte binding arm and molecular beacon binding arm, and (c) the oligonucleotide analyte binding arm that is complementary and selectively hybridizes with particular region of analyte. On binding analyte, molecular beacon gives off fluorescent signals.



This invention also consists of another group of binary probes based on aptamers that bind to a dye. This group of probe comprises of a) an analyte binding arm, flanked by a linker; b) a linker flanked by a first stem sequence; c) the first stem sequence that is complementary to a first stem sequence on the second strand, and that is flanked by a dye-binding nucleotide sequence, (d) the dye-binding nucleotide sequence that is flanked by a second stem sequence, and (e) the second stem sequence that is complementary to a second stem sequence on the second strand, and a second oligonucleotide strand that is antiparallel to the first. On hybridization to oligonucleotide analyte the fluorescence of the dye increases dramatically and is easily detected and measured.





Applications:

• Detect single nucleotide polymorphism

• Nucleic acid analysis by hybridization technique.

• Developed into molecular diagnostic assay kit.





Advantages:

• Reduced cost for multiple assays.

• Highly reliable in detecting SNP under physiological conditions.

• High selectivity of nucleic acid detection.

• The assay can be performed at room temperature.

• Increased detection efficacy and sensitivity, which allows detection of nucleic acid in the presence of 50 fold excess of oligonucleotide containing a single base substitution this allowing the allele specific PCR.





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.



Kolpashchikov D. "Binary Malachite Green Aptamer for Fluorescent Detection of Nucleic Acids"; J. Am. Chem. Soc. 2005; 127(36): 12442-12443.




Other Links:

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

Further Information
Peter Golikov
Email: TechTransfer@columbia.edu

File Number: 1941