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Exonuclease patents



      
           
This page is updated frequently with new Exonuclease-related patent applications. Subscribe to the Exonuclease RSS feed to automatically get the update: related Exonuclease RSS feeds. RSS updates for this page: Exonuclease RSS RSS


Targeting oligonucleotides and related methods for modulating fxn rna

Rana Therapeutics

Targeting oligonucleotides and related methods for modulating fxn rna

Pseudocircularization oligonucleotides for modulating rna

Rana Therapeutics

Pseudocircularization oligonucleotides for modulating rna


Date/App# patent app List of recent Exonuclease-related patents
08/20/15
20150232925 
 Sequencing method patent thumbnailSequencing method
Typically the biological probe employed comprises a single-stranded nucleotide region the ends of which are attached to two different oligonucleotide regions wherein at least one of the oligonucleotide regions comprises detectable elements having a characteristic detection property and wherein the detectable elements are so arranged on the oligonucleotide region that the detectable property is essentially undetectable in the probe's unused state. In a most preferred embodiment the probe is labelled with multiple fluorophores and further comprises a restriction enzyme recognition site generated by the binding of the target single nucleotide to the single-stranded nucleotide region.

08/20/15
20150232847 
 Targeting oligonucleotides and related methods for modulating fxn rna patent thumbnailTargeting oligonucleotides and related methods for modulating fxn rna
Aspects of the invention relate to methods for increasing gene expression in a targeted manner. In some embodiments, methods and compositions are provided that are useful for posttranscriptionally altering protein and/or rna levels in a targeted manner.
Rana Therapeutics, Inc.


08/20/15
20150232846 
 Pseudocircularization oligonucleotides for modulating rna patent thumbnailPseudocircularization oligonucleotides for modulating rna
Aspects of the invention relate to methods for increasing gene expression in a targeted manner. In some embodiments, methods and compositions are provided that are useful for posttranscriptionally altering protein and/or rna levels in a targeted manner.
Rana Therapeutics, Inc.


08/20/15
20150232845 
 5' targeting oligonucleotides for modulating rna patent thumbnail5' targeting oligonucleotides for modulating rna
Aspects of the invention relate to methods for increasing gene expression in a targeted manner. In some embodiments, methods and compositions are provided that are useful for posttranscriptionally altering protein and/or rna levels in a targeted manner.
Rana Therapeutics, Inc.


08/20/15
20150232844 
 Methods for modulating rna using 5' targeting oligonucleotides patent thumbnailMethods for modulating rna using 5' targeting oligonucleotides
Aspects of the invention relate to methods for increasing gene expression in a targeted manner. In some embodiments, methods and compositions are provided that are useful for posttranscriptionally altering protein and/or rna levels in a targeted manner.
Rana Therapeutics, Inc.


08/13/15
20150225715 
 3' targeting oligonucleotides for modulating rna patent thumbnail3' targeting oligonucleotides for modulating rna
Aspects of the invention relate to methods for increasing gene expression in a targeted manner. In some embodiments, methods and compositions are provided that are useful for posttranscriptionally altering protein and/or rna levels in a targeted manner.
Rana Therapeutics, Inc.


08/06/15
20150218535 
 Recombinant polymerases with increased phototolerance patent thumbnailRecombinant polymerases with increased phototolerance
Provided are compositions comprising recombinant dna polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties include increased resistance to photodamage, and can also include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like.
Pacific Biosciences Of California


06/25/15
20150176067 
 Microarray system with improved sequence specificity patent thumbnailMicroarray system with improved sequence specificity
The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple snps (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets.

06/18/15
20150167071 
 Nucleic acid sequence analysis patent thumbnailNucleic acid sequence analysis
Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid.
Pacific Biosciences Of California, Inc.


06/18/15
20150166968 
 Fusion polymerases patent thumbnailFusion polymerases
Fusion polypeptides having a heterologous 5′-3′ exonuclease domain linked to a polymerase that does not naturally have 5′-3′ exonuclease activity, as well as methods of their use are provided. Other aspects are also disclosed..
Bio-rad Laboratories, Inc.


06/04/15
20150152482 

Multiplex targeted amplification using flap nuclease


Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified.
Affymetrix, Inc.


05/14/15
20150133338 

Hydrolysis probes


Methods and compositions for the detection and quantification of nucleic acids are provided. In one embodiment, a sample is contacted with a primer complementary to a first region of a target nucleic acid and a probe complementary to a second region of the target nucleic acid downstream of the first region under conditions suitable for hybridization of the target nucleic acid with the primer and the probe.

04/30/15
20150119261 

Enrichment of target sequences


Methods and compositions are provided for enriching for target sequences from a population of nucleic acids, that includes: combining in solution, a population of nucleic acids and a target isolation probe wherein the target isolation probe comprises an affinity binding domain; permitting a single stranded region of the target isolation probe to hybridize to all or a portion of a target sequence in the population of nucleic acids; selectively immobilizing the hybridized nucleic acids from the population containing the target sequences by associating the target isolation probe with a capture domain and removing unbound material; removing non-target sequences from the 3′ end of the target sequence by means of one or more 3′ exonucleases thereby generating a blunt ended duplex or a staggered end at the 3′ end of the target sequence; optionally ligating a 3′ duplex adaptor or a duplex end of a hairpin adaptor to the 3′ end of the target sequence and the 5′ end of the target isolation probe; extending the 3′ end of the target isolation probe to form a blunt end or a staggered end at the 5′ end of the target sequence suitable for ligating and ligating an adapter to the 5′ end of the target sequence and the 3′ extended end of the target isolation probe.. .
New England Biolabs, Inc.


03/26/15
20150087557 

Enzyme composition for dna end repair, adenylation, phosphorylation


Enzyme compositions and their method of use that provide ready-to-use master mixtures. The compositions comprise a modified thermophilic dna polymerase lacking 5′-3′ and 3′-5′ exonuclease activity premixed with t4 dna polymerase, klenow fragment and t4 polynucleotide kinase and all other necessary components, including reaction buffer and nucleoside triphosphates, required to perform dna blunting, phosphorylation, and single nucleotide extension reactions in one tube and in two steps.
Thermo Fisher Scientific Baltics Uab


03/19/15
20150079629 

Nucleic acid which is stabilized against decomposition


The invention relates to a nucleic acid which is stabilised against decomposition by exonucleases. Said nucleic acid contains the following constituents: a) a code sequence coding for a defined protein, b) optionally, a promoter sequence controlling the expression of the code sequence, and c) at least one molecule a added to an end of the linear sequence containing the constituents a and b, said molecule being linked to a non-immobilised, volumic molecule b..
Siemens Building Technologies Ag


03/12/15
20150072342 

Methods of using fet labeled oligonucleotides that include a 3'-5' exonuclease resistant quencher domain and compositions for practicing the same


Methods and compositions are provided for detecting a primer extension product in a reaction mixture. In the subject methods, a primer extension reaction is conducted in the presence of a polymerase having 3′→5′ exonuclease activity and at least one fet labeled oligonucleotide probe that includes a 3′→5′ exonuclease resistant quencher domain.
Life Technologies Corporation


02/26/15
20150056629 

Compositions, systems, and methods for detecting a dna sequence


Provided are compositions, systems, and methods that employ one or more fusion protein pairs, wherein each fusion protein within a fusion protein pair comprises a sequence-specific nucleic acid binding protein, such as sequence-specific cas9 protein (e.g., a crispr), a sequence specific transcription activator-like enhancer (“tale”) protein, a sequence specific homing endonuclease (“he”; a/k/a meganuclease), a three prime exonuclease (“trex”), and/or a sequence specific zinc finger (“zf”) protein, which sequence-specific nucleic acid binding protein is operably linked to one half of a split-reporter molecule, such as a split-fluorescent reporter molecule, a split-luminescent reporter molecule, a förster resonance energy transfer (fret) reporter molecule, or a bioluminescence resonance energy transfer (bret) reporter molecule.. .

02/19/15
20150050738 

Compositions and methods for modulating rna


Aspects of the invention relate to methods for increasing gene expression in a targeted manner. In some embodiments, methods and compositions are provided that are useful for posttranscriptionally altering protein and/or rna levels in a targeted manner.
Rana Therapeutics, Inc.


12/25/14
20140378340 

Methods for genotyping


Novel methods and kits are disclosed for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences, for example, to discriminating between alleles at polymorphic positions in a genome. Complexity reduction can be accomplished by extension of a capture probes followed by amplification of the extended capture probe using common primers.
Affymetrix, Inc.


12/25/14
20140378327 

Real-time multiplexed hydrolysis probe assay using spectrally identifiable microspheres


Methods and compositions for the detection and quantification of nucleic acids are provided. In one embodiment, a sample is contacted with a primer and a quencher-probe complementary to a target nucleic acid.
Luminex Corporation


12/25/14
20140377767 

Methods and compositions for improving efficiency of nucleic acids amplification reactions


The present invention provides methods and compositions for improving the efficiency of nucleic acid amplification reactions. The invention encompasses hybrid polymerases that show increased processivity over wild type polymerases as well as decreased exonucleases activity.
Bio-rad Laboratories, Inc.


11/27/14
20140349286 

Exonuclease cycling assay


The present invention relates to a novel method for detecting a target polynucleotide having a target sequence, comprising hybridizing the target polynucleotide with a probe to form a hybrid; exposing the hybrid to a 5′ exonuclease so that the probe in the hybrid is digested and the target polynucleotide is dissociated from the digested probe; repeating the hybridization step and the digestion step; and detecting the digested probes. The presence of the digested probes indicates the presence of the target polynucleotide..

11/06/14
20140329880 

Exonuclease resistant polynucleotide and related duplex polynucleotides, constructs, compositions, methods and systems


Provided herein are exonuclease resistant polynucleotides and related constructs, compositions, methods and systems.. .

10/23/14
20140315211 

Methods for suppression pcr


Provided herein are approaches for the detection, identification, and/or selective amplification of specific target species or target variants of nucleic acid sequences, even within an excess of unwanted similar sequences or variants. These approaches include methods, assays, and kits for suppression pcr that require, in part, dna polymerase that lacks 5′-3′ exonuclease activity, and a pcr primer, termed a forward selective primer or a nunchaku primer.

10/02/14
20140296082 

Dna polymerase variants with reduced exonuclease activity and uses thereof


Compositions and methods are described to modify family b dna polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo−” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic dna polymerase..

09/25/14
20140287468 

Enrichment of target sequences


Methods and compositions are provided for enriching for target sequences from a population of nucleic acids, that includes combining in solution, a population of nucleic acids and a target isolation probe wherein the target isolation probe includes an affinity binding domain; permitting a single stranded region of the target isolation probe to hybridize to all or a portion of a target sequence in the population of nucleic acids; selectively immobilizing the hybridized nucleic acids from the population containing the target sequences by associating the target isolation probe with a capture domain and removing unbound material; and removing from the 3′ end of the target sequence, a non-target sequence by means of one or more 3′ single strand specific exonucleases. Target enrichment may be used to detect variations in nucleotide sequence for detecting phenotypic changes related to health or disease..

06/19/14
20140171334 

Gene analysis method using sdl-pcr


According to the sdl-pcr method of the present invention, non-specific amplification can be minimized by removing non-ligated probes or genomic dna using a tag, and separation can be achieved within a shorter time compared to a separation method that is performed using exonuclease. In addition, ligation, separation and polymerase chain reaction processes can be performed in a single solution in a single tube, and thus a plurality of genes can be amplified at the same time in an accurate and rapid manner..

06/05/14
20140154748 

Thermostable chimeric nucleic acid polymerases and uses thereof


Novel thermostable chimeric nucleic acid polymerases and methods for their generation and use are disclosed. It is shown that these chimeric nucleic acid polymerases, such as dna polymerases, can be constructed using enzymatically active domains, isolated from different proteins or chemically synthesized.

05/08/14
20140127680 

Single molecule sequencing with two distinct chemistry steps


Methods, compositions, and systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3′ hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3′ hydroxyl leaving group preferentially after it has been incorporated.

05/01/14
20140120576 

Nucleic acid which is stabilized against decomposition


The invention relates to a nucleic acid which is stabilised against decomposition by exonucleases. Said nucleic acid contains the following constituents: a) a code sequence coding for a defined protein, b) optionally, a promoter sequence controlling the expression of the code sequence, and c) at least one molecule a added to an end of the linear sequence containing the constituents a and b, said molecule being linked to a non-immobilised, volumic molecule b..

04/10/14
20140101789 

Plants tolerant to abiotic stress


The present invention provides genetically modified plants having increased tolerance to environmental abiotic stress, particularly to salt stress and water stress (drought). The tolerant genetically modified plants of the invention include transgenic plants overexpressing at least one inositol polyphosphate 5-phosphatase selected from 5tpase7 5tpase9 and plants having altered expression of the endonuclease/exonuclease/phosphatase (eep) protein zeep1..

04/03/14
20140094375 

Recombinant polymerases for incorporation of protein shield nucleotide analogs


Provided are compositions comprising recombinant dna polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing or nucleic acid amplification. Such properties include enhanced performance with large nucleotide analogs, increased stability, increased readlength, and improved detection of modified bases, and can also include resistance to photodamage, enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased accuracy, altered speed, increased cosolvent resistance, and the like.

04/03/14
20140094374 

Recombinant polymerases with increased readlength and stability for single-molecule sequencing


Provided are compositions comprising recombinant dna polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing or nucleic acid amplification. Such properties include increased stability, increased readlength, enhanced performance with large nucleotide analogs, and improved detection of modified bases, and can also include resistance to photodamage, enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased accuracy, altered speed, increased cosolvent resistance, and the like.

01/30/14
20140030721 

Exonuclease enabled proximity extension assays


The present invention relates to a proximity probe based detection assay (“proximity assay”) for an analyte in a sample, specifically a proximity probe extension assay (pea), an in particular to an improvement in the method to reduce non-specific “background” signals, wherein the improvement comprises the use in such assays of a component comprising 3′ exonuclease activity, said method comprising: (a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte; (b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex; (c) contacting said sample with a component comprising 3′ exonuclease activity; (d) extending the 3′ end of at least one nucleic acid domain of said duplex to generate an extension product, wherein the step may occur contemporaneously with or after step (c); and (e) amplifying and detecting the extension product.. .

11/28/13
20130316927 

Microarray system with improved sequence specificity


The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple snps (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets.

11/14/13
20130302794 

Nucleic acid detection by oligonucleotide probes cleaved by both exonuclease and endonuclease


Disclosed is a method in the fields of biochemistry and molecular biology. The method is related to improve cleavage kinetics of labeled oligonucleotide probes and, consequently, increases signal-to-noise ratio in detecting nucleic acids..

09/26/13
20130252827 

Detection of target nucleic acid sequences using dual-labeled immobilized probes on solid phase


The present invention relates to a novel method for detection of target nucleic acid sequences on a solid phase using dual-labeled immobilized probes and its resistance to a 5′ to 3′ exonuclease activity of a dna polymerase. Because the label is remained on the solid substrate by resistance to nucleases due to labeling of a base component the internal nucleotide, the present invention requires no consideration of a suitability of position of the label for remaining on the solid substrate.

08/29/13
20130225451 

Materials and methods for the synthesis of error-minimized nucleic acid molecules


The present invention provides materials and methods useful for error correction of nucleic acid molecules. In one embodiment of the invention, a first plurality of double-stranded nucleic acid molecules having a nucleotide mismatch are fragmented by exposure to a molecule having unidirectional mismatch endonuclease activity.

08/22/13
20130217007 

Recombinant polymerases with increased phototolerance


Provided are compositions comprising recombinant dna polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties include increased resistance to photodamage, and can also include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like.

08/01/13
20130196327 

Dna polymerase variants with reduced exonuclease activity and uses thereof


Compositions and methods are described to modify family b dna polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo−” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic dna polymerase..

05/23/13
20130130352 

Contamination-free reagents for nucleic acid amplification


Methods and kits for generating contamination-free reagents and reagent solutions for use in nucleic acid amplification are provided. Methods include processing of polymerase solutions, nucleotide solutions and primer solutions to render contaminating nucleic acid inert.

05/23/13
20130130323 

Prevention and alleviation of steric hindrance during single molecule synthesis


The present invention provides compositions and methods for reducing steric hindrance in the product of nucleic acid polymerase reaction. Methods and compositions of the invention encompass application of exonucleases, endonucleases, and uracil-dna glycosylases to a nucleic acid polymerase reaction such that newly formed nucleic acid strands are modified (e.g., cleaved) while the polymerase reaction continues to proceed..

05/16/13
20130123117 

Capture probe and assay for analysis of fragmented nucleic acids


Disclosed is an efficient and scalable method for targeted resequencing and variant identification of nucleic acids such as genomic dna found in single stranded, fragmented form, such as in a clinical sample of formalin-fixed, paraffin-embedded (ffpe) tissue. The method uses a large number of capture probes mixed with the sample in the presence of a 5′ to 3′ exonuclease, a 3′ to 5′ exonuclease, a ligase, and a universal amplification oligonucleotide that hybridizes to the various capture probes.

04/04/13
20130085078 

Hydrolysis probes


Methods and compositions for the detection and quantification of nucleic acids are provided. In one embodiment, a sample is contacted with a primer complementary to a first region of a target nucleic acid and a probe complementary to a second region of the target nucleic acid downstream of the first region under conditions suitable for hybridization of the target nucleic acid with the primer and the probe.

02/14/13
20130040860 

Microarray system with improved sequence specificity


The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple snps (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets.

01/31/13
20130029331 

Novel fluorescence-based assay for the rapid detection and quantification of deoxyribonucleoside triphosphates


The inventors have developed a rapid and sensitive fluorescence-based assay to quantify dntps. This assay relies on the principle that incorporation of a limiting dntp is required for primer-extension and polymerase-mediated 5-3′ exonuclease hydrolysis of a quenched fluorophore-labeled probe resulting in fluorescence.



Popular terms: [SEARCH]

Exonuclease topics: Exonuclease, Polymerase, Nucleic Acid, Nucleotide, Dna Polymerase, Sequencing, Nucleic Acids, Recombinant, Endonuclease, Amplification, Oligonucleotide, Hydrolysis, Fluorophore, Dna Molecules, Oligonucleotide Probe

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