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IP Watch: Enzo, JHU, Cepheid, Sequenom, GC, GeneNews, BD, TriLink, and PentaBase Win US Patents

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This story has been updated from a previously posted version.

Enzo Diagnostics has been awarded US Patent No. 8,133,989, "Nucleic acid primer/construct compositions."

Elazar Rabbani, Jannis Stavrianopolous, James Donegan, Jack Coleman, and Marleen Walner are named as inventors on the patent.

Provides novel processes for amplifying nucleic acid sequences of interest, including linear and non-linear amplification. In linear amplification, a single initial primer or nucleic acid construct is used to carry out the amplification process. In non-linear amplification, a first initial primer or nucleic acid construct is used with a subsequent initial primer or nucleic acid construct. The invention also provides other non-linear amplification processes wherein a first initial primer or nucleic acid construct is deployed with a second initial primer or nucleic acid construct to amplify the specific nucleic acid sequence of interest and its complement. A singular primer or a singular nucleic acid construct capable of non-linear amplification can also be used to carry out non-linear amplification. The patent also discloses a post-termination labeling process for nucleic acid sequencing, which is based upon the detection of tagged molecules that are covalently bound to chemically reactive groups provided for chain terminators. The patent also describes a process for producing nucleic acid sequences having decreased thermodynamic stability to complementary sequences; and discloses unique nucleic acid polymers, other novel compositions, kits, and the like.


Johns Hopkins University School of Medicine has been awarded US Patent No. 8,133,986, "Methylated CpG island amplification."

Jean-Pierre Issa, Stephen Baylin, and Minory Toyota are named as inventors on the patent.

Provides a method for identifying a methylated CpG-containing nucleic acid. The method involves contacting a nucleic acid with a methylation-sensitive restriction endonuclease that cleaves unmethylated PcG sites; and contacting the sample with an isoschizomer of the methylation-sensitive restriction endonuclease, which cleaves both methylated and unmethylated CpG sites. The method also includes amplifying the CpG-containing nucleic acid using CpG-specific oligonucleotide primers. The patent also provides a method for detecting an age-associated disorder by identifying a methylated CpG-containing nucleic acid. The patent further provides a method for evaluating the responses of a cell to an agent; as well as kits useful for detecting a CpG-containing nucleic acid.


PentaBase has been awarded US Patent No. 8,133,984, "Oligonucleotides comprising signalling pairs and hydrophobic nucleotides, stemless beacons, for detection of nucleic acids, methylation status and mutants of nucleic acids."

Ulf Christensen is named as inventor on the patent.

Relates to novel oligonucleotides comprising a signalling pair and at least two hydrophobic nucleotides. The oligonucleotide analogues are useful for detecting the status of nucleic acid sequences, such as their presence, expression, methylation, and/or mutation. In particular they are useful for detecting single point mutations and other sequences where the variation between the correct target and other targets may vary by as little as one nucleotide. The invention also relates to new ways of detecting sequence differences and optimizing conditions by using oligonucleotide analogues and readily available instruments. In particular the invention relates to specifically quantifying target nucleic acids, or detecting one sequence over others that may vary by as little as one nucleotide, using oligonucleotides or oligonucleotide analogues comprising a signalling pair and at least two hydrophobic nucleotides, such as a nucleotide analogue comprising an intercalator.


Cepheid has been awarded US Patent No. 8,133,703, "Closed-system multi-stage nucleic acid amplification reactions."

Jesus Ching, Ronald Chang, Douglas Dority, Jian Zhang, James Wang, Wendy Wong, Kendra Paul, and Reuel Van Atta are named as inventors on the patent.

Describes systems, methods, and an apparatus for carrying out multi-stage amplification reactions, especially under fluidly closed conditions. In one aspect, the methods are carried out in a fluidly closed reaction system that permits the isolation of a portion of a first reaction mixture and its use as a sample or specimen in a second reaction mixture, thereby substantially avoiding interfering effects that the first reaction components may have in the second reaction if both reaction mixtures were simply combined together. In this aspect, the systems, methods, and apparatus of the invention may be used with any amplification reaction that permits multiple stages of amplification based on the use of nested primers.


Sequenom has been awarded US Patent No. 8,133,701, "Detection and quantification of biomolecules using mass spectrometry."

Dirk Van Den Boom is named as inventor on the patent.

Describes, in part, a method for detecting a target nucleic acid using oligonucleotides detectable by mass spectrometry. This method uses the 5'-to-3' nuclease activity of a nucleic acid polymerase to cleave annealed oligonucleotide probes from hybridized duplexes and release labels for detection by mass spectrometry. This process is easily incorporated into a PCR amplification assay, the patent's abstract states. The method also includes embodiments directed to quantitative analysis of target nucleic acids.


GC Corporation of Japan has been awarded US Patent No. 8,133,677, "Method for measuring the number of oral Lactobacillus, and a PCR primers-probe set used for the same."

Yuko Matsumoto and Yoko Ishihara are named as inventors on the patent.

Describes a real-time PCR assay capable of measuring the number of lactobacilli present in an oral cavity, in a short amount of time. The method uses a combination of a forward primer comprising an oligonucleotide part of at least 15 sequential bases in the base sequence of any one of four specified base sequences; a reverse primer comprising an oligonucleotide part of at least 15 sequential bases in the base sequence of any one of three specified base sequences; and a probe for measuring the number of oral lactobacillus, comprising an oligonucleotide part of at least 10 sequential bases in the base sequence of any one of eight specified base sequences.


Gene News has been awarded US Patent No. 8,133,674, "Method of profiling gene expression in a subject having diabetes;" and US Patent No. 8,133,675, "Method of profiling gene expression in a subject having an infectious disease."

Choong-Chin Liew is named as inventor on the patents.

The '674 patent describes detection and measurement of gene transcripts in blood. More specifically, it describes reverse transcriptase PCR analysis performed on a drop of blood to detect, diagnose, and monitor diseases using tissue-specific primers. The invention also describes methods by which delineation of the sequence and/or quantitation of the expression levels of disease-associated genes allows for an immediate and accurate diagnostic/prognostic test for disease or to assess the effect of a particular treatment regimen.

The '675 patent generally describes the same inventions used in the context of infectious disease instead of diabetes.


HandyLab (Becton Dickinson) has been awarded US Patent No. 8,133,671, "Integrated apparatus for performing nucleic acid extraction and diagnostic testing on multiple biological samples."

Jeff Williams, Kalyan Handique, and Kerry Wilson are named as inventors on the patent.

Relates to systems for extracting polynucleotides from multiple samples, particularly from biological samples; and to systems that subsequently amplify and detect the extracted polynucleotides. The technology more particularly relates to microfluidic systems that carry out PCR on multiple samples of nucleotides of interest within microfluidic channels, and detect those nucleotides.


TriLink Biotechnologies has been awarded US Patent No. 8,133,669, "Chemically modified nucleoside 5'-triphosphates for thermally initiated amplification of nucleic acid."

Alexandre Lebedev and Inna Koukhareva are named as inventors on the patent.

Provides methods and compositions for nucleic acid replication. The methods involve the use of 3'-substituted nucleoside 5'-triphosphates or 3'-substituted terminated primers in nucleic acid replication reactions. In certain aspects, the methods are accomplished by using 3'-substituted NTPs and/or 3'-substituted terminated primers that provide utility in nucleic acid replication. In preferred embodiments, the NTPs and/or primers are substituted at the 3'-position with particular heat-labile chemical groups such as ethers, esters, or carbonate esters.

The Scan

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To Watch the Variants

Scientists told US lawmakers that SARS-CoV-2 variants need to be better monitored, the New York Times reports.

Nature Papers Present Nautilus Genome, Tool to Analyze Single-Cell Data, More

In Nature this week: nautilus genome gives peek into its evolution, computational tool to analyze single-cell ATAC-seq data, and more.