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IP Update: Recent Patents Related to PCR, Sample Prep, and Nucleic Acid Amplification: Dec 3, 2009

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US Patent 7,625,746. Method of denaturing and fragmenting DNA or RNA using ultrasound. Inventors: Tim Patno; Tom Westberg; Michael Halblander; Emily Beeson; Benjamin Rush. Assignee: Nanosphere.

Protects a method and apparatus for processing a DNA or RNA sample within a sample-processing module. The method includes the steps of providing a sample well within the sample processing module that contains the DNA or RNA sample, coupling ultrasonic energy from an external source into the sampling well, and denaturing and fragmenting the DNA or RNA sample using the ultrasonic energy.


US Patent 7,625,705. Methods and compositions for detection of a target nucleic acid sequence utilizing a probe with a 3' flap. Inventors: Andrew Firmin; Joseph Sorge. Assignee: Hologic.

Covers compositions, kits, and methods of generating a signal that indicates the presence of a target nucleic acid sequence in a sample by forming a cleavage structure. The cleavage structure is formed by incubating a sample containing a target nucleic acid with a downstream probe that forms a 3' flap when hybridized to the target. The cleavage structure is cleaved with a 3' nuclease and a detectable signal is produced, the patent abstract states.


US Patent 7,622,296. Apparatus and method for multiplex analysis. Inventors: Victor Joseph; Amjad Huda; Alnoor Shivji; Jie Zhou. Assignee: WaferGen.

Describes miniaturized instruments for conducting chemical reactions with a controlled reaction temperature. The invention provides chips and optical systems for performing and monitoring temperature-dependent chemical reactions. The apparatus and methods "are particularly useful for high-throughput and low-cost amplification of nucleic acids," the patent abstract states.


US Patent 7,622,281. Methods and compositions for clonal amplification of nucleic acid. Inventors: Mostafa Ronaghi; Foad Mashayekhi. Assignee: The Board of Trustees of the Leland Stanford Junior University.

Protects methods and compositions relating to labeling and amplifying a nucleic acid molecule. According to the patent claims, the method first attaches a unique antiprimer to each nucleic acid molecule to be amplified, then hybridizes each of those molecules to a solid surface that is attached to a primer that is complementary to the antiprimer, which forms a single captured DNA fragment on each solid surface. The method then extends the hybridized molecule to form a double-stranded fragment, which is denatured. This single-stranded captured DNA fragment is labeled by nucleotide extension and isolated. The method then attaches additional primers to the solid surface and uses them to amplify the captured DNA fragment.


US Patent 7,622,280. Emulsion compositions. Inventors: Phillip Holliger; Farid Ghadessy. Assignee: 454 Life Sciences.

Describes method for increasing the concentration of a nucleic acid molecule based on first forming microcapsules from a water-in-oil emulsion and then amplifying the nucleic acid molecule in the microcapsules to form amplified copies of the nucleic acid molecule, "wherein the amplification employs a thermal cycling process, thereby increasing the concentration of the nucleic acid molecule in the microcapsules," according to the patent claims.


US Patent 7,622,253. Classification of patients having diffuse large b-cell lymphoma based upon gene expression. Inventors: Ronald Levy; Mark Wechser; Izidore Lossos; Robert Tibshirani; Ash Alizadeh; David Botstein. Assignee: None.

Protects methods and kits for classifying patients with diffuse large B-cell lymphoma based on gene expression measured by real-time quantitative RT-PCR. "Correlating expression values of the plurality of genes in a tumor sample from the patient to reference expression values obtained from DLBCL patients can stratify patients in the classification groups," the patent abstract states. The methods and kits can be used to predict overall patient survival.


US Patent 7,622,076. Microfluidic analysis system. Inventors: Mark Davies; Tara Dalton. Assignee: Stokes Bio.

Describes a microfluidic analysis system that performs PCR analysis on a biological sample. The system uses a centrifuge to separate the sample into DNA and RNA constituents. The biological sample exits the centrifuge enveloped in a carrier fluid. This is pumped by a flow controller to a thermal stage, which has a number of microfluidic devices with thermal zones in which the sample is heated or cooled by heat conduction. "Thus, the carrier fluids envelope the sample, control its flowrate, and control its temperature without need for moving parts at the micro scale," the patent abstract states.


US Patent 7,618,776. Rolling circle replication reporter systems. Inventor: Paul Lizardi. Assignee: Yale University.

Protects a method for amplifying nucleic acid sequences that is "useful for detecting specific nucleic acids in a sample with high specificity and sensitivity" and a low level of background signal, according to the patent abstract. A preferred form of the method consists of a DNA ligation operation, which circularizes a specially designed nucleic acid probe molecule; an amplification operation, which is rolling circle replication of the circularized probe; and a detection operation "using any of the conventional detection systems for nucleic acids such as detection of fluorescent labels, enzyme-linked detection systems, antibody-mediated label detection, and detection of radioactive labels," the abstract states. "Major advantages of this method are that the ligation step can be manipulated to obtain allelic discrimination, the DNA replication step is isothermal, and signals are strictly quantitative because the amplification reaction is linear and is catalyzed by a highly processive enzyme."


US Patent 7,618,780. Use of mass labeled probes to detect target nucleic acids using mass spectrometry. Inventor: Andrew Thompson. Assignee: Trillion Genomics.

Covers the use of mass-labeled probes to characterize nucleic acids by mass spectrometry. The invention provides methods of detecting the presence of a target nucleic acid in a sample using a circularizing probe that includes a mass tag. Additional methods of detecting the presence of a target nucleic acid are also described in which a probe-detection sequence in the circularizing probe is detected with a probe attached to a mass tag.


US Patent 7,618,773. Headloop DNA amplification. Inventors: Keith Rand; Peter Laurence Molloy. Assignee: Commonwealth Scientific and Industrial Research Organization

Describes a method for the selective amplification of a target nucleic acid in a sample. The method amplifies nucleic acids via oligonucleotide primers that comprise two regions: a primer region that can prime and extend on target and non-target nucleic acids; and a region that is an inverted repeat of an internal sequence of an amplicon of a non-target nucleic acid, but contains at least one mismatch to the corresponding internal sequence, if present, of an amplicon of the target nucleic acid.


US Patent 7,615,625. In vitro amplification of nucleic acid molecules via circular replicons. Inventor: Jeffrey Auerbach. Assignee: Replicon.

Covers methods and compositions suitable for the in vitro amplification of nucleic acid molecules via enzymatic. The preferred method employs circular rather than linear replicons. The patent describes means for producing circular replicons from linear reactants.


US Patent 7,615,620. Detection system for PCR assay. Inventor: Philip Robinson. Assignee: KBiosciences.

Provides a detection system for a PCR process using FRET, which comprises at least two single-labeled oligonucleotide sequences of differing melting temperature that hybridize to one another in free solution to form a fluorescent quenched pair. Upon introduction of a complementary sequence to one or both sequences, the pair generates a measurable signal, with one of the sequences having a melting temperature that is below the annealing temperature of the PCR process and the other not being below the annealing temperature of the PCR process.


US Patent 7,615,346. Rapid and efficient capture of DNA from sample without using cell lysing reagent. Inventors: Robert Belly; Jianbo Sun. Assignee: Ortho-Clinical Diagnostics.

"Nucleic acids can be made available for amplification or other treatment after admixture of a sample with specific weakly basic polymers to form a precipitate with the nucleic acids at acidic pH," the patent abstract states. After removing non-precipitated materials, the pH is made basic to release the nucleic acids from the polymer. "This method for preparing specimen samples is simple and quite rapid, and the released nucleic acids can be further treated in hybridization assays or amplification procedures" without surfactants or other cell-lysing reagents, according to the abstract.


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