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IP Watch: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: Jul 13, 2011

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Nishikawa Rubber has been awarded US Patent No. 7,977,055, "Method for amplification of a nucleotide sequence."

Katsunori Nakashima and Isao Ohiso are named as inventors on the patent.

Provides a method for selectively amplifying a target nucleic acid and a method for detecting a nucleic acid, which are useful as a method for synthesizing nucleic acid. More specifically, the patent describes the endonuclease V-dependent amplification method, which selectively amplifies a target nucleic acid in a sample by using an oligonucleotide primer containing a base that can be recognized by an endonuclease V, with the endonuclease V and a DNA polymerase having a strand displacement activity. The patent also describes use of the method for detecting a nucleic acid.


Virco has been awarded US Patent No. 7,977,053, "Circular probe amplification using energy-transfer primers."

David Thomas is named as inventor on the patent.

Provides methods and kits for the rapid exponential amplification of nucleic acid molecules using a padlock probe. The invention improves upon existing methods for amplifying padlock probes by eliminating or delaying the appearance of artifact products that cause false positive results, and also increases the sensitivity and speed of the assay. The patent further provides nucleic acid amplification primers containing non-informative base analogs.


Bioarray Solutions has been awarded US Patent No. 7,977,050, "Nucleic acid amplification with integrated multiplex detection."

Michael Seul, Nataliya Korzheva, Jiacheng Yang, and Yi Zhang are named as inventors on the patent.

Describes a method mediated with in vitro transcription, or IVT, which permits miniaturization of multiplexed DNA and RNA analysis, and in which elongation-mediated multiplexed analysis of polymorphisms is used as the analysis step. Also describes a method mediated with IVT for selecting a designated strand from T7-tagged double-stranded DNA wherein the selected strand forms the template for RNA synthesis. In one embodiment, double-stranded DNA incorporating the T7 (or other) promoter sequence at the 3' end or the 5' end is produced, for example, by PCR amplification of genomic DNA. The patent also discloses nested PCR designs permitting allele analysis in combination with strand selection by IVT. Further, in one embodiment of a homogeneous format for transcription-mediated amplification and multiplexed detection, encoded microparticles display looped capture probe configurations permitting the generation of a signal upon capture of RNA product and real-time assay monitoring. This latter method may be particularly suited for viral or pathogen detection, the patent's abstract states.


Aisin Seiki and Riken have been awarded US Patent No. 7,973,131, "Extreme thermophile single-stranded DNA binding mutant protein, and nucleic acid isothermal amplification method of use thereof."

Yasushi Shigemori, Takehiko Shibata, and Tsutomu Mikawa are named as inventors on the patent.

Describes a technology that allows the inhibition of non-specific amplification during nucleic acid amplification in an isothermal amplification reaction, such that amplification efficiency is increased. The invention is an extreme thermophile single-stranded DNA-binding mutant protein, having an amino acid sequence that expresses a function that can contribute to increasing the amplification efficiency of a template nucleic acid in an isothermal amplification reaction system. The system uses a strand displacement polymerase having in its amino acid sequence a mutation site where a mutation involving at least one of a deletion, substitution, addition, and insertion of one or more amino acids in the sequence of the extreme thermophile single-stranded DNA binding protein has occurred.


Abacus Diagnostica has been awarded US Patent No. 7,972,838, "Method for stabilizing assay reagents, reagent container with stabilized assay reagents and use thereof

Teemu Korpimaki, Timo Lovgren, and Jussi Nurmi are named as inventors on the patent.

Describes a reagent container having an inner surface upon which at least two reagents are dried, with the first reagent dried on a first area separate from a second area where the second reagent is dried. The first and second reagents are a nucleic acid polymerase and its substrate. The patent also discloses a method that includes dispensing at least the first and second reagents onto separate areas of the inner surface of the reagent container, and removing excess water from the reagents. The reagent container can be used in a PCR assay; an assay that utilizes a reverse transcriptase; a reverse transcriptase PCR; an immuno-PCR assay; a nucleic acid sequence-based assay; a proximity ligation assay; a ligase chain reaction assay; a rolling circle amplification assay; and a strand displacement amplification assay.


Sigma-Aldrich has been awarded US Patent No. 7,972,828, "Stabilized compositions of thermostable DNA polymerase and anionic or zwitterionic detergent."

Brian Ward, Ernest Mueller, Jessica Copeland, and Deborah Vassar are named as inventors on the patent.

Provides compositions, methods, and kits for protecting thermostable DNA polymerase during amplification reactions conducted at a temperature ranging from about 40°C to greater than 100°C. The composition comprises a thermostable DNA polymerase and an anionic detergent or zwitterionic detergent.


Illumina has been awarded US Patent No. 7,972,820, "Isothermal amplification of nucleic acids on a solid support."

Pascal Mayer is named as inventor on the patent.

Discloses methods for isothermal amplification of nucleic acids by the means of a solid support. The methods are useful for applications needing high throughput, in particular nucleic acid sequencing.


Lawrence Livermore National Security has been awarded US Patent No. 7,972,818, "Flow cytometric detection method for DNA samples."

Shanavaz Nasarabandi, Richard Langlois, and Kodumudi Venkateswaran are named as inventors on the patent.

Discloses two methods of rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3, as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.


OncoMedx has been awarded US Patent No. 7,972,817, "Method enabling use of extracellular RNA extracted from plasma or serum to detect, monitor, or evaluate cancer."

Michael Kopreski is named as inventor on the patent.

Relates to the use of extracellular RNA found circulating in the plasma or serum fraction of blood. Specifically, this invention enables the extraction of circulating RNA from plasma or serum and utilizes nucleic acid amplification assays for the identification, detection, inference, monitoring, or evaluation of any such RNA. Further, the invention allows the qualitative or quantitative detection of extracellular RNA circulating in the plasma or serum of humans.


Brandeis University has been awarded US Patent No. 7,972,786, "Detection and analysis of influenza virus."

Cristina Hartshorn, Kenneth Pierce, Arthur Reis, John Rice, Aquiles Sanchez, and Lawrence Wangh are named as inventors on the patent.

Describes an assay comprising more than one primer pair and more than one detection probe, and a low-copy number synthetic amplicon corresponding to each of the primer pairs. The assay can detect and distinguish between various sub-types and strains of an influenza virus using any suitable nucleic acid amplification technique. The patent also describes related kits and methods.


Epigenomics has been awarded US Patent No. 7,972,784, "Method for quantification of methylated DNA."

Fabian Model is listed as inventor on the patent.

Relates to a method for quantifying methylated cytosines in DNA. In the first step, unmethylated cytosines in the DNA to be analyzed are chemically converted into uracil while 5-methylcytosines remain unchanged. In a second step the converted DNA is amplified methylation-specifically in a real-time PCR reaction using a methylation-specific probe. Finally the amount of uniformly methylated DNA is calculated by combining criteria derived from the shape of the real-time curve and from the signal intensity. The method is preferably used for diagnosing and/or prognosing adverse events for individuals, for distinguishing cell types and tissues, or for investigating cell differentiation, the patent's abstract states.

The Scan

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Limited Rapid Testing

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Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.