Abstract: The present invention provides methods, compositions, and kits for detecting the presence or absence of target sequences in a sample, where the sample also contains interfering sequences that are similar or identical to the target sequences. In particular, the present invention provides blocker oligonucleotides that at least partially inhibit the formation of invasive cleavage structures with the interfering sequences but do not substantially inhibit the formation of invasive cleavage structures with the target sequences.
Type:
Grant
Filed:
November 3, 2006
Date of Patent:
January 27, 2009
Assignee:
Third Wave Technologies, Inc.
Inventors:
Poonam Agarwal, Robert W. Kwiatowski, Jr.
Abstract: The invention relates to compositions for generating a signal indicative of the presence of a target nucleic acid in a sample, where the compositions include an RNA polymerase, a FEN nuclease, and a probe.
Abstract: The invention relates to a nucleic acid marker ladder which is a restriction endonuclease digest, wherein a nucleic acid restriction endonuclease digest is a collection of nucleic acid fragments resulting from complete digestion of one or more nucleic acids by one or more restriction endonucleases; the restriction endonuclease digest contains at least 3 fragments; and the size of the fragments in base pairs is a multiple of an integer, wherein the integer is 10 or more.
Abstract: The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. Selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. In another aspect primers that are complementary to a subset of the fragments after adaptor ligation are used for amplification. Reduced complexity samples generated by the disclosed methods may be interrogated for the genotypes of SNPs in the sample.
Abstract: Methods and compositions for inhibiting and/or inactivating nucleases by employing nuclease inhibitors are provided. The nuclease inhibitors comprise anti-nuclease antibodies and non-antibody nuclease inhibitors. The anti-nuclease antibodies of the present invention may be a polyclonal or monoclonal antibodies, and may be anti-ribonuclease antibodies, anti-deoxyribonuclease antibodies, or antibodies to non-specific nucleases. A preferred embodiment comprises at least two nuclease inhibitors, and is referred to as a nuclease inhibitor cocktail. In some specific embodiments, the invention concerns methods of performing in vitro translation comprising obtaining a first nuclease inhibitor, which inhibitor is further defined as an anti-nuclease antibody, and placing the anti-nuclease antibody in an in vitro translation reaction. In many cases, the in vitro translation reaction comprises at least one nuclease, which may be a ribonuclease, a deoxyribonuclease, or a nonspecific nuclease.
Type:
Grant
Filed:
December 6, 2006
Date of Patent:
November 4, 2008
Assignee:
Applera Corporation
Inventors:
W. Antoni Kudlicki, Matthew M. Winkler, Brittan L. Pasloske
Abstract: Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.
Type:
Grant
Filed:
October 27, 2006
Date of Patent:
October 28, 2008
Assignee:
University of Rochester
Inventors:
Benjamin L. Miller, Christopher M. Strohsahl
Abstract: The invention provides a method useful for detection of genetic disorders. The method comprises determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality. The present invention also provides a non-invasive method for the detection of chromosomal abnormalities in a fetus. The invention is especially useful as a non-invasive method for determining the sequence of fetal DNA. The invention further provides methods of isolation of free DNA from a sample.
Abstract: The present invention relates to methods and compositions for analyzing nucleic acids. In particular, the present invention provides methods and compositions for the detection and characterization of nucleic acid sequences and sequence changes. The methods of the present invention permit the detection and/or identification of genetic polymorphism such as those associated with human disease and permit the identification of pathogens (e.g., viral and bacterial strain identification).
Type:
Grant
Filed:
September 5, 2006
Date of Patent:
September 30, 2008
Assignee:
Third Wave Technologies, Inc.
Inventors:
Fang Dong, Victor I. Lyamichev, James R. Prudent, Lance Fors, Bruce P. Neri, Mary Ann D. Brow, Todd A. Anderson, James E. Dahlberg
Abstract: Nucleic acid sequences and methods for detecting HIV-1 nucleic acid (LTR and pol sequences) in biological samples by detecting amplified nucleic acids are disclosed. Kits comprising nucleic acid oligomers for amplifying HIV-1 nucleic acid present in a biological sample and detecting the amplified nucleic acid are disclosed.
Type:
Grant
Filed:
July 24, 2006
Date of Patent:
September 16, 2008
Assignee:
Gen-Probe Incorporated
Inventors:
Gary G. Bee, Yeasing Y. Yang, Dan Kolk, Cristina Giachetti, Sherrol H. McDonough
Abstract: This invention provides compositions and methods for genetic testing of an organism and for correlating the results of the genetic testing with a unique marker that unambiguously identifies the organism. The markers may be internal markers, such as for example single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), or other sites within a genomic locus. Alternatively, the markers may be external, such that they are separately added to the genetic sample before testing.
Type:
Grant
Filed:
May 22, 2006
Date of Patent:
September 16, 2008
Assignee:
Bio Array Solutions Ltd.
Inventors:
Ghazala Hashmi, Michael Seul, Joachim Messing
Abstract: The invention relates to a method for synthesizing templated molecules attached to the templated which directed the synthesis thereof. The method involves a template, a scaffold functional entity and a functional entity attached to a building block, which, in turn, is attached the template. The scaffold functional entity and the functional entity of the building block are both provided with complementary dimerization domains allowing the functional entities to come into close proximity when the complementary domains interact with to each other. The method may be used for generating libraries of templated molecules which may be selected for biological activity.
Type:
Grant
Filed:
March 14, 2003
Date of Patent:
August 19, 2008
Assignee:
Nuevolution A/S
Inventors:
Henrik Pedersen, Anette Holtmann, Thomas Franch, Alex Haahr Gouliaev, Jakob Felding
Abstract: This invention relates to the field of detecting interacting molecules. The invention provides a set of a first and a second probe, each such probe provided with a dye allowing energy transfer; at least one probe provided with a reactive group allowing juxtaposing the first and second probe. A method is provided for detecting at least two interacting molecules at the single cell level using of a set of probes according to the invention.
Type:
Grant
Filed:
May 5, 2005
Date of Patent:
August 19, 2008
Assignee:
Erasmus Universteit Rotterdam
Inventors:
Jacobus Johannes Maria van Dongen, Frank Jakob Theodor Staal
Abstract: Method for detecting macromolecular biopolymers using a unit for immobilizing macromolecular biopolymers, in which the unit is provided with first molecules serving as capture molecules.
Type:
Grant
Filed:
May 7, 2004
Date of Patent:
August 19, 2008
Assignee:
Siemens Aktiengesellschaft
Inventors:
Christian Paulus, Petra T. Schindler-Bauer
Abstract: A method for detecting and measuring the concentration of biomolecules in solution, utilizing a conducting electrode in contact with a solution containing target biomolecules, with a film with controllable pore size distribution characteristics applied to at least one surface of the conducting electrode. The film is functionalized with probe molecules that chemically interact with the target biomolecules at the film surface, blocking indicator molecules present in solution from diffusing from the solution to the electrode, thereby changing the electrochemical response of the electrode.
Abstract: Method and device to collect multiplex data simultaneously in analyte detection and analyze the data by experimentally trained software (machine-learning) is disclosed. Various ways (magnetic particles and microcoils) are disclosed to collect multiple reporter (tag) signals. Multiplex detection can increase the biomolecule analysis efficiency by using small sample size and saving assay reagents and time. Machine learning and data analysis schemes are also disclosed. Multiple affinity binding partners, each labeled by a unique reporter, are contacted with a sample and a green spectrum is taken to detect multiple reporter signals. The spectrum is deconvoluted by experimentally trained software to identify multiple analytes.
Type:
Grant
Filed:
September 1, 2005
Date of Patent:
August 12, 2008
Assignee:
Intel Corporation
Inventors:
Xing Su, Lei Sun, Mineo Yamakawa, Jingwu Zhang, Qing Ma, Tae-Woong Koo, Richard Jones
Abstract: The present invention provides new probes for the detection of prostate cancer cells. The probes bind selectively with target polynucleotide sequences selected from the group consisting of 2q, 4q, 5q, 6q, 10p, 15q, 1q, 2p, 3q, 3p, 4q, 6p, 7p, 7q, 9q, 11p, 16p, and 17q.
Type:
Grant
Filed:
November 4, 2005
Date of Patent:
August 5, 2008
Assignee:
The Regents of the University of California
Abstract: A detection system and methods for improving the ability of the detection system to recognize labels that are disposed on a polymer. Embodiments of the invention include schemes for selecting emitters and labels used within the system in a manner that allows an increase in the number of distinct labels that can be used together in a system. In other embodiments, the detection system and methods are directed to identifying portions of a detection signal that may be associated with extra labels residing within a detection zone. In other embodiments, the detection system and methods relate to using wide field imaging detectors while reducing out of focus noise contributions to detection signals of the system. Still, other embodiments relate to the use of linear array detectors to detect labels.
Abstract: The present invention relates to the use of self-assembled monolayers with mixtures of conductive oligomers and insulators to detect target analytes.
Abstract: A method including providing an initial test sample including a primary material and a relatively smaller amount of at least one adventitious material; combining the initial test sample with a standard addition of at least one adventitious material to form a final test sample, wherein the standard addition has a known amount of genetically modified adventitious material; and analyzing the final test sample to determine the % GMO of the primary material and the % GMO of the adventitious material.
Abstract: A biosensor unit that can be wall mounted in a location to perform testing of ambient air for bio-contaminants. This unit could contain an air filter for collecting contaminants and a micro-laboratory on a chip or otherwise situated within the unit to perform DNA or RNA binding tests for specific biological targets. Information from such units distributed within an environment could be communicated to one or more central locations via the internet or other communication means to be logged or recorded or to produce reports or alarms.