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

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Applied Biosystems (now Life Technologies) has been awarded US Patent No. 8,036,832, "Automatic threshold setting and baseline determination for real-time PCR."

David Woo, Clinton Lewis, and Nasser M. Abbasi are named as inventors on the patent.

Describes a system and methods for quantitating the presence of nucleic acid sequences via real-time PCR. In one aspect, the methods "may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction," the patent abstract states.


Helixis (now Illumina) has been awarded US Patent No. 8,035,811, "Devices and methods for visualization of a sample in a microplate."

Arkadiy Silbergleit, Adrian Fawcett, Michael Andrew Swartz, and Kevin Daley Simmons are named as inventors on the patent.

Protects a microplate with a plurality of wells, as well as and methods and systems comprising such microplates, in which an individual well comprises an opaque or non-transparent surface at or near the bottom of the well. The microplates can provide "improved visualization of the process of filling a well with a liquid reagent and can be configured to perform chemical analysis, such as PCR or nucleic acid detection.


Steven Albert Benner, Daniel Hutter, Nicole Aurora Leal, and Fei Chen have been awarded US Patent No. 8,034,923, "Reagents for reversibly terminating primer extension."

Discloses processes that use 3'-reversibly terminated nucleoside triphosphates to analyze DNA for purposes other than sequencing using cyclic reversible termination. These processes are based on the "unexpected ability of terminal transferase to accept these triphosphates as substrates, the unexpected ability of polymerases to add reversibly and irreversibly terminated triphosphates in competition with each other, the development of cleavage conditions to remove the terminating group rapidly, in high yield, and without substantial damage to the terminated oligonucleotide product, and the ability of reversibly terminated primer extension products to capture groups," according to the patent abstract.


Abbott Laboratories has been awarded US Patent No. 8,034,920, "Nucleic acid primers and probes for detecting breast cells."

Natalie A. Solomon and Lisa A Roberts-Rapp are named as inventors on the patent.

Provides polynucleotides that are useful as amplification primers and hybridization probes for detecting BS106 target sequence in a test sample. The primers and probes can be used to perform homogeneous, real time reverse-transcriptase PCR to detect BS106 target sequence in a test sample, the patent abstract states.


Canon has been awarded US Patent No. 8,034,919, "Probe, probe set, probe carrier, and testing method."

Nobuhiro Tomatsu, Toshifumi Fukui, Nobuyoshi Shimizu, and Atsushi Takayanagi are named as inventors on the patent.

Describes a probe, a set of probes, and a probe carrier on which the probe or the set of probes is immobilized. The probe or the set of probes is capable of detecting fungus of the same species and distinguishing the species of the fungus. The probe is an oligonucleotide probe for detecting DNA of the pathogenic fungus Arthroderma benhamiae and includes base sequences specific to the species.


Canon has been awarded US Patent No. 8,034,918, "Probe, probe set, probe carrier, and testing method

Nobuhiro Tomatsu, Toshifumi Fukui, Nobuyoshi Shimizu, and Atsushi Takayanagi are named as inventors on the patent.

Describes a probe, a set of probes, and a probe carrier on which the probe or the set of probes is immobilized. The probe or the set of probes is capable of detecting fungus of the same species and distinguishing the species of the fungus. The probe is an oligonucleotide probe for detecting DNA of the pathogenic fungus Cryptococcus neoformans and includes base sequences specific to the species.


Geneohm Sciences Canada (now part of BD) has been awarded US Patent No. 8,034,588, "Species-specific, genus-specific and universal DNA probes and amplification primers to rapidly detect and identify common bacterial and fungal pathogens and associated antibiotic resistance genes from clinical specimens for diagnosis in microbiology laboratories."

Michel G. Bergeron, Francois J. Picard, Marc Ouellette, and Paul H. Roy are named as inventors on the patent.

The patent protects methods and kits for the "specific and ubiquitous" detection of Streptococcus agalactiae, according to the patent abstract.


The Mayo Foundation for Medical Education and Research has been awarded US Patent No. 8,034,577, "Methods and probes for detecting esophageal cancer."

Kevin Halling, Larry E. Morrison, and Shannon Brankley are named as inventors on the patent.

Describes probe sets and methods of using probes and probe sets for selectively detecting high-grade dysplasia and esophageal adenocarcinoma or low-grade dysplasia from biologic samples. Methods of the invention include contacting a biological sample obtained from a subject with a set of chromosomal probes to selectively detect an esophageal carcinoma or precursor lesion in the sample.


Gen-Probe has been awarded US Patent No. 8,034,570, "Tagged oligonucleotides and their use in nucleic acid amplification methods."

Michael M. Becker, Kristin W. Livezey, and Wai-Chung Lam are named as inventors on the patent.

Describes methods for selective amplification of target nucleic acid sequence using a tagged oligonucleotide comprising a target-hybridizing sequence that hybridizes to a 3'-end of the target nucleic acid and a tag sequence situated 5' to the target hybridizing sequence. "The tagged oligonucleotide is hybridized to the target nucleic acid and, after reducing the effective concentration of unhybridized tagged oligonucleotide having an active form, a primer extension reaction is initiated to produce a primer extension product," the patent abstract states. "Further amplification also utilizes a first oligonucleotide that hybridizes to the 3' end of the complement of the target nucleic acid and a second oligonucleotide that hybridizes to the complement of the tag sequence." The patent also covers reaction mixtures that comprise the tagged oligonucleotide hybridized to target nucleic "and substantially free of an active form of unhybridized tagged oligonucleotide."


Biotex has been awarded US Patent No. 8,034,569, "Methods for molecular detection."

George Jackson and Christopher Quan are named as inventors on the patent.

Provides methods for molecular detection that rely on target-specific molecular probes. Target-specific molecular probes can include single-stranded DNA or RNA Aptamers and may bind with relatively high specificity to a given target. In one aspect, the method comprises "a molecular probe paired to a reporter molecule wherein the molecular probe impairs the amplification of the reporter molecule in the absence of the target molecule," the patent abstract states.


NuGen Technologies has been awarded US Patent No. 8,034,568, "Isothermal nucleic acid amplification methods and compositions."

Nurith Kurn and Shenglong Wang are named as inventors on the patent.

Describes methods and compositions related to the amplification of target polynucleotide sequences as well as total RNA and total DNA amplification. "In some embodiments, the methods and compositions also allow for the immobilization and capture of target polynucleotides with defined 3' and or 5' sequences to solid surfaces," the patent abstract states. The polynucleotides can be amplified or eluted for downstream processing and in some cases they can be used for high-throughput sequencing of nucleotide sequences related to target DNA or target RNA.


Gen-Probe has been awarded US Patent No. 8,034,554, "Methods and compositions to detect nucleic acids in a biological sample."

Michael M. Becker and Mehrdad R. Majlessi are named as inventors on the patent.

Describes a method for separating a target nucleic acid from a sample by using at least one capture probe oligonucleotide that contains a target-complementary region and a member of a binding pair that attaches the target nucleic acid to an immobilized probe on a capture support. This forms "a capture hybrid that is separated from other sample components before the target nucleic acid is released from the capture support and hybridized to a detection probe to form a detection hybrid that produces a detectable signal that indicates the presence of the target nucleic acid in the sample," the patent abstract states.


Promega has been awarded US Patent No. 8,030,034, "Nucleic acid purification with a binding matrix."

Rex M. Bitner, Michelle N. Mandrekar, and Paula R. Brisco are named as inventors on the patent.

Protects methods, kits, and compositions for generating purified RNA samples and purified DNA samples. In particular, the methods use a binding matrix that preferentially binds DNA or RNA in the presence of an acidic dilution buffer, or a binding matrix that comprises acid zeolites.

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