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Allawi, WI

Hatim Allawi, Madison, WI US

Patent application numberDescriptionPublished
20080293046RNA detection assays - The present invention provides novel cleavage agents and polymerases for the cleavage and modification of nucleic acid. The cleavage agents and polymerases find use, for example, for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. In some embodiments, the 5′ nuclease activity of a variety of enzymes is used to cleave a target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.11-27-2008
20110104682RNA DETECTION ASSAYS - The present invention provides novel cleavage agents and polymerases for the cleavage and modification of nucleic acid. The cleavage agents and polymerases find use, for example, for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. In some embodiments, the 5′ nuclease activity of a variety of enzymes is used to cleave a target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.05-05-2011
20120122105REAL TIME CLEAVAGE ASSAY - A cleavage-based real-time PCR assay method is provided. In general terms, the assay method includes subjecting a reaction mixture comprising a) PCR reagents for amplifying a nucleic acid target, and b) flap cleavage reagents for performing a flap cleavage assay on the amplified nucleic acid target to two sets of thermocycling conditions. No additional reagents are added to the reaction between said first and second sets of cycles and, in each cycle of the second set of cycles, cleavage of a flap probe is measured.05-17-2012

Patent applications by Hatim Allawi, Madison, WI US

Hatim Allawi, Middleton, WI US

Patent application numberDescriptionPublished
20120122088METHYLATION ASSAY - A method for detecting a methylated genomic locus is provided. In certain embodiments, the method comprises: a) treating a nucleic acid sample that contains both unmethylated and methylated copies of a genomic locus with an agent that modifies cytosine to uracil to produce a treated nucleic acid; b) amplifying a product from the treated nucleic acid using a first primer and a second primer, wherein the first primer hybridizes to a site in the locus that contain methylcytosines and the amplifying preferentially amplifies the methylated copies of the genomic locus, to produce an amplified sample; and c) detecting the presence of amplified methylated copies of the genomic locus in the amplified sample using a flap assay that employs an invasive oligonucleotide having a 3′ terminal G or C nucleotide that corresponds to a site of methylation in the genomic locus.05-17-2012
20120122106Mutation Detection Assay - A method of sample analysis is provided. In certain embodiments, the method involves: a) amplifying a product from a sample that comprises both wild type copies of a genomic locus and mutant copies of the genomic locus that have a point mutation relative to said wild type copies of the genomic locus, to produce an amplified sample, where: i. the amplifying is done using a first primer and a second primer; and ii. the first primer comprises a 3′ terminal nucleotide that base pairs with the point mutation and also comprises a nucleotide sequence that is fully complementary to a sequence in the locus with the exception of a single base mismatch within 6 bases of the 3′ terminal nucleotide; and b) detecting the presence of said product in said amplified sample using a flap assay that employs an invasive oligonucleotide. A kit for performing the method is also provided.05-17-2012

Hatim T. Allawi, Madison, WI US

Patent application numberDescriptionPublished
20090078574CHARGE TAGS AND THE SEPARATION OF NUCLEIC ACID MOLECULES - The present invention relates to novel phosphoramidites, including positive and neutrally charged compounds. The present invention also provides charge tags for attachment to materials including solid supports and nucleic acids, wherein the charge tags increase or decrease the net charge of the material. The present invention further provides methods for separating and characterizing molecules based on the charge differentials between modified and unmodified materials.03-26-2009
20090142754RNA Detection Assays - The present invention provides novel cleavage agents and polymerases for the cleavage and modification of nucleic acid. The cleavage agents and polymerases find use, for example, for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. In some embodiments, the 5′ nuclease activity of a variety of enzymes is used to cleave a target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.06-04-2009
20090253142COMPOSITIONS AND METHODS FOR ANALYSIS OF NUCLEIC ACID MOLECULES DURING AMPLIFICATION REACTIONS - The present invention provides systems, methods and kits for performing a detection assay (e.g., invasive cleavage assay) in combination with an amplification assay (e.g., PCR), where the detection assay employs enzyme footprint probes with relatively short (e.g., 6-12 bases) analyte-specific regions configured to provide a preferred footprint length of duplex for use with a particular nucleic acid modifying enzyme. In some embodiments, such assays are used for target quantification, and in other embodiments, such assays are used for genotyping. In certain embodiments, the use of such short probes allows for assays with increased dynamic range.10-08-2009
20090299641METHODS AND APPLICATIONS FOR TARGET QUANTIFICATION - The present invention provides methods and software applications for quantifying a target in an experimental sample by collecting and processing initial signal data from the experimental sample and at least two standard control samples containing known target copy numbers. In this regards, the present invention allows the quantification of target copy number in the experimental sample.12-03-2009

Patent applications by Hatim T. Allawi, Madison, WI US

Hatim Taysir Allawi, Madison, WI US

Patent application numberDescriptionPublished
20090075256Nucleic Acid Accessible Hybridization Site Identification Using Mass Spectrometry - The present invention relates to methods and compositions for analyzing nucleic acids, and in particular, methods and compositions for detection and characterization of nucleic acid sequences and sequence changes using mass spectrometry. The present invention also provides methods and compositions for identifying oligonucleotides with desired hybridization properties to nucleic acid targets containing secondary structure using mass spectrometry.03-19-2009
20100285488T-STRUCTURE INVASIVE CLEAVAGE ASSAYS, CONSISTENT NUCLEIC ACID DISPENSING, AND LOW LEVEL TARGET NUCLEIC ACID DETECTION - The present invention relates to systems, methods and kits for low-level detection of nucleic acids, detecting at least two different viral sequences in a single reaction vessel, and increasing the dynamic range of detection of a viral target nucleic acid in a sample. The present invention also relates to T-structure invasive cleavage assays, as well as T-structure related target dependent non-target amplification methods and compositions. The present invention further relates to methods, compositions, devices and systems for consistent nucleic acid dispensing onto surfaces.11-11-2010

Patent applications by Hatim Taysir Allawi, Madison, WI US