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IP Watch: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: Sep 30, 2010

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Lawrence Livermore National Laboratory of Livermore, Calif., has been awarded US Patent No. RE41,780, entitled "Chemical amplification based on fluid partitioning in an immiscible liquid," a reissuance of US Patent No. 7,041,481.

Brian Anderson, Billy Colston, and Chris Elkin are named as inventors on the patent.

Describes a system for nucleic acid amplification of a sample by partitioning the sample into and performing PCR on the partitioned sections. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample, performing PCR on the partitioned sections, and detecting and analyzing the partitioned sections, according to the patent's abstract.


TrovaGene of San Diego, Calif., has been awarded US Patent No. 7,803,929, "Kits for diagnosis and monitoring of pathogenic infection by analysis of cell-free pathogenic nucleic acids in urine."

Hovsep Melkonyan, Angela Cannas, Louis Tomei, and Samuil Umansky are named as inventors on the patent.

Relates to a method for diagnosing and/or monitoring a bacterial or parasitic infection by detecting and quantifying transrenal nucleic acids derived from bacterial pathogenic agents or parasites in urine. The detection method optionally includes isolating and purifying the nucleic acids from urine by methods known in the art including pairing with molecular probes that are specific for the pathogenic agents, PCR hybridization, PCR, nested PCR, single-strand conformational polymorphism analysis, ligase chain reaction, and strand displacement amplification. The patent also provides diagnostic kits based on these detection methods.


Rockefeller University of New York has been awarded US Patent No. 7,803,596, "Enzyme derived from thermophilic organisms that functions as a chromosomal replicase, and preparation and uses thereof."

Olga Yurieva, John Kuriyan, Michael O'Donnell, and David Jeruzalmi are named as inventors on the patent.

Relates to the identification of a DNA polymerase in a thermophile that functions as a chromosomal replicase. The specific enzyme is a holoenzyme III that has been identified in Thermus thermophilus, and corresponds to Polymerase III in E. coli. The patent discloses genes and the polypeptides corresponding to T. thermophilus gamma, tau, epsilon, alpha, and beta subunits; as well as probes, vectors, methods of preparation, and the methods of use. The enzymes and their components are particularly well-suited for use in procedures for the preparation of DNA, such as PCR, because of the speed and accuracy that they are able to achieve, according to the patent's abstract.


Gen-Probe has been awarded US Patent No. 7,803,581, "Alkaline shock-based preparation of nucleic acids."

Kui Gao, Michael Becker, Wen Wu, and Jeffrey Linnen are named as inventors on the patent.

Discloses a method of preparing a biological sample appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions, which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The method can improve detection of some target nucleic acids without substantially compromising detectability of others, and is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions, according to the patent's abstract.


Human Genetic Signatures of North Ryde, Australia, has been awarded US Patent No. 7,803,580, "Amplification blocker comprising intercalating nucleic acids containing intercalating pseudonucleotides."

Douglas Millar is the sole inventor named on the patent.

Discloses an amplification blocker comprising an intercalating nucleic acid containing two or more internal intercalating pseudonucleotides capable of blocking or reducing nucleic acid amplification. Also discloses use of the amplification blocker to block or reduce nucleic acid amplification.

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Riken of Saitama, Japan, and DNAForm of Kanagawa, Japan, have been awarded US Patent No. 7,803,579, "Process for amplifying nucleic acid."

Yasumasa Mitani, Akio Yamane, Yuko Shibata, and Yoshihide Hayashizaki are named as inventors on the patent.

Relates to a process for synthesizing or amplifying efficiently a nucleic acid comprising a target sequence. The process involves providing a primer comprising in its 3'-end portion a sequence (Ac') which hybridizes a sequence (A) in the 3'-end portion of the target nucleic acid sequence, and in the 5'-side of the sequence (Ac') a sequence (B') that hybridizes the complementary sequence (Bc) of a sequence (B) positioned in the 5'-side of the sequence (A) on the target nucleic acid sequence.


The University of Utah and Idaho Technologies of Salt Lake City have been awarded US Patent No. 7,803,551, "Amplicon melting analysis with saturation dyes."

Carl Wittwer and Virginie Dujols are named as inventors on the patent.

Provides methods for nucleic acid analysis wherein a target nucleic acid that is at least partially double stranded is mixed with a double-stranded DNA-binding dye having a percent saturation of at least 50 percent to form a mixture. In one embodiment, the nucleic acid is amplified in the presence of the dsDNA-binding dye, and in another embodiment a melting curve is generated for the target nucleic acid by measuring fluorescence from the dsDNA- binding dye as the mixture is heated. The patent also provides dyes for use in nucleic acid analysis and methods for making dyes.


Rubicon Genomics of Ann Arbor, Mich., has been awarded US Patent No. 7,803,550, "Methods of producing nucleic acid molecules comprising stem loop oligonucleotides."

Vladimir Makarov, Emmanuel Kamberov, and Brendan Tarrier are named as inventors on the patent.

Discloses the preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome, the patent's abstract states.


Cepheid has been awarded US Patent No. 7,803,549, "Controls for primers in multiplex amplification reactions."

David Swenson is the sole inventor named on the patent.

Provides methods and compositions for confirming the integrity of primers and other components of amplification reactions, including multiplex amplification reactions.


Toshiba of Tokyo has been awarded US Patent No. 7,803,544, "Method of detecting amplification product or target nucleic acid."

Naoko Nakamura and Keiko Ito are named as inventors on the patent.

Describes a method of designing primers for use in a method of detecting an amplification product by hybridizing it with a probe. In the method, the amplification product is amplified from a target nucleic acid with the primers, including placing F3, F2, and F1 regions in this order from a 5' terminal side; and Bc, B2c, and B1c regions in this order from a 3' terminal side. The method additionally involves placing an FP region in the region from the F2 to F1 regions, and/or a BPc region in the region from the B2c to B1c regions in the target nucleic acid. In addition, the method involves determining the respective regions in such a manner that the FP and F2 regions and/or the BPc and B2c regions have an unoverlapping region of at least 10 bases and overlapping regions of fewer than 10 bases, and designing the primers according to the regions.


Chang Gung University of Taiwan has been awarded US Patent No. 7,803,543, "Methods and kits for the detection of nucleotide mutations using peptide nucleic acid as both PCR clamp and sensor probe."

Chiuan-Chian Chiou and Ji-Dung Luo are named as inventors on the patent.

Discloses a method for determining whether a target polynucleotide sequence contained in a nucleic acid sample has one or more nucleotide variations in a selected region thereof. The method involves using a pair of primers that allow the formation of a PCR product having a sequence covering that of the selected region of the target polynucleotide sequence via a PCR process; and a peptide nucleic acid that acts as a PCR clamp as well as a sensor probe. The patent also discloses a kit that includes the pair of primers and the PNA for use in determining the presence of one or more nucleotide variations in the target polynucleotide sequence.


Samsung Electronics of Korea has been awarded US Patent No. 7,803,539, "Method of isolating and purifying nucleic acids using immobilized hydrogel or PEG-hydrogel copolymer."

Chang-eun Yoo, Joon-ho Kim, Kyu-youn Hwang, Hun-joo Lee, Hee-kyun Lim, and Jun-hong Min; are named as inventors on the patent.

Provides a method of isolating and purifying nucleic acids using an immobilized hydrogel or polyethylene glycol-hydrogel copolymer. The method includes: immobilizing a functional group-containing hydrogel or PEG-hydrogel copolymer on a substrate; adding to that a mixed sample solution containing a salt and nucleic acids to bind the nucleic acids to the hydrogel or the PEG-hydrogel copolymer; washing the nucleic acid-bound hydrogel or PEG-hydrogel copolymer; and eluting the nucleic acids from the hydrogel or the PEG-hydrogel copolymer using an elution solvent. According to the patent's abstract, this method allows binding and elution of nucleic acids with no addition of a separate chemical substance, and minimizes an effect on a subsequent process such as PCR. Furthermore, the amount and intensity for binding nucleic acids can be adjusted according to PEG concentration, and the presence of a hydrogel compound on a substrate enables patterning.


Apodemus of Kalmar, Sweden, and the Robert-Koch Institut of Berlin have been awarded US Patent No. 7,803,525, "Detection method for Ljungan virus."

Bo Niklasson, Andreas Nitsche, Oliver Mantke, and Matthias Niedrig are named as inventors on the patent.

Relates to a method for specifically detecting Ljungan virus using quantitative real-time reverse transcriptase PCR. The invention also provides kits for performing the method.

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