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IP Update: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: May 6, 2010

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Birch Biomedical Research has been awarded US Patent No. 7,709,188, "Multi-allelic detection of SARS-associated coronavirus."

Leondios Kostrikis is the sole inventor listed on the patent.

The invention relates to a multiple-allelic reverse transcriptase real-time PCR assay for coronaviruses including the SARS virus. Multiple target sequences within the SARS-CoV, S, E, M, and N genes are identified. The use of the four different targets enhances the likelihood that the fundamental genetic drift of the virus will not lead to a false negative result. The patent envisions multiplex assay formats that allow for early diagnosis of a SARS infection. The assay would be useful in the context of monitoring treatment regimens, screening potential anti-SARS agents, and similar applications requiring qualitative and quantitative determinations, according to the patent abstract.


Cornell University has been awarded US Patent No. 7,709,201, "Detection of nucleic acid differences using endonuclease cleavage/ligase resealing reactions and capillary electrophoresis or microarrays."

Inventors listed on the patent are Francis Barany, Hanna Pincas, and Jianmin Huang.

According to its abstract, the patent is directed to various methods for detecting DNA sequence differences, including single nucleotide mutations or polymorphisms, one or more nucleotide insertions, and one or more nucleotide deletions. The method involves preparing labeled heteroduplex PCR fragments containing base mismatches. Endonuclease cleaves the heteroduplex PCR fragments both at the position containing the variation (one or more mismatched bases) and, to a lesser extent, at non-variant (perfectly matched) positions. Ligation of the cleavage products with a DNA ligase corrects non-variant cleavages and thus substantially reduces background. This is then followed by a detection step in which the reaction products are detected, and the position of the sequence variations are determined.


The National Food Research Institute of Japan and Asahi Breweries have been awarded US Patent No. 7,709,232, "Methods of quantitative detection of genetic recombinants and standard molecules for the methods."

Inventors listed on the patent are Akihiro Hino, Takeshi Matsuoka, Hideo Kuribara, Tomoaki Yoshimura, Yoichiro Shindo, Satoshi Futo, and Machiko Ogawa.

The patent relates to a method of using PCR to quantitatively detect a genetic recombinant. The method comprises performing PCR for the DNA sequence specific to the recombinant and the endogenous DNA sequence shared by the species corresponding to the recombinant. The method uses, as a standard molecule, a molecule containing the DNA sequence specific to the recombinant and the endogenous DNA sequence shared by the species on the single molecule. Using the method, the total content ratio of the genetic recombinants and the individual content ratio of the genetic recombinant in a population containing plural genetic recombinant lines can be quantified, according to the patent's abstract.


3M Innovative Properties has been awarded US Patent No. 7,709,249, "Multiplex fluorescence detection device having fiber bundle coupling multiple optical modules to a common detector."

Inventors listed on the patent are William Bedingham, Peter Ludowise, and Barry Robole.

The patent describes techniques for detecting multiple target species in real-time PCR. For example, the patent describes a system that includes a data-acquisition device coupled to a detection device. The detection device includes a rotating disk having a plurality of process chambers having a plurality of species that emit fluorescent light at different wavelengths. The device further includes a plurality of optical modules. Each of the optical modules is optically configured to excite the species and capture fluorescent light emitted by the species at different wavelengths. A fiber optic bundle coupled to the plurality of optical modules conveys the fluorescent light from the multiple optical modules to a single detector.


The US Centers for Disease Control and Prevention and the Department of Health and Human Services have been awarded US Patent No. 7,709,626, "Primer for nucleic acid detection."

Inventors listed on the patent are Jothikumar Narayanan and Vincent Hill.

The patent provides universal labeled primers for detecting and amplifying nucleic acid molecules. The primers can be attached to the 5'-end of a target sequence-specific primer. In particular examples, the universal primer includes a labeled nucleotide flanked on both sides by a nucleotide whose complement nucleotides change a detectable signal from the label when the universal primer hybridizes with its complementary nucleic acid molecule. Also disclosed are methods of using the universal primer in nucleic acid amplification, such as real-time PCR.


Lawrence Livermore National Laboratory has been awarded US Patent No. 7,711,491, "Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis."

Inventors listed on the patent are Jennifer Vandersall, Shea Gardner, and David Clague.

The patent describes a computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature, and concentration of species.

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