Nucleic acid labeling compounds
Granted: January 18, 2005
Patent Number:
6844433
Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
Methods for identifying and using maintenance genes
Granted: January 11, 2005
Patent Number:
6841348
This invention provides methods for discovering maintenance genes and for using maintenance genes. In one embodiment, the expression of at least three maintenance genes are measured and used as reference (or control) for comparing the expression of target genes in two or more biological samples.
Phosphite ester oxidation in nucleic acid array preparation
Granted: December 21, 2004
Patent Number:
6833450
Methods are provided for preparing nucleic acid arrays on a support. In these methods a plurality of nucleic acids are synthesized on the support and the synthesis steps include oxidizing a phosphite triester nucleic acid linkage to a phosphate triester nucleic acid linkage using a solution about 0.005 to about 0.05 M iodine in a mixture comprising water and organic solvent.
Nucleic acid probe libraries
Granted: December 14, 2004
Patent Number:
6830890
Libraries of unimolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA. In a related aspect, the present invention provides libraries of conformationally restricted probes on a solid support. The probes are restricted in their movement and flexibility using…
Integrated nucleic acid diagnostic device
Granted: December 14, 2004
Patent Number:
6830936
The present invention provides a miniaturized integrated nucleic acid diagnostic device and system. The or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. For example, the device can integrate several or all of the operations involved in sample acquisition and storage, sample preparation and sample analysis, within a single integrated unit. The device is useful in a variety of applications, and most notably, nucleic acid…
Nucleic acid affinity columns
Granted: December 7, 2004
Patent Number:
6828104
This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different…
Computer software system, method, and product for scanned image alignment
Granted: December 7, 2004
Patent Number:
6829376
An image alignment tool is described for adjusting the alignment of a grid with an image. An initial grid aligner determines an initial, approximately aligned, position of the grid. An intensity scorer determines, for each of a plurality of test grid elements of the plurality of grid elements, a set of intensity scores. Each member of the set is based, at least in part, on intensities of pixels of one or more image features within the test grid element in one of the initial or additional…
Porous silica substrates for polymer synthesis and assays
Granted: November 30, 2004
Patent Number:
6824866
Methods are provided for making and using thin films of porous silica substrates to synthesize arrays of polymers. Methods are also provided for assaying such polymers on porous silica substrates. The porous silica substrates offer an increase in array density and signal enhancement over conventional flat glass substrates. Examples of polymers that can be synthesized and assayed include biological polymers such as nucleic acids, polynucleotides, polypeptides, and polysaccharides. Arrays…
Method and system for providing a probe array chip design database
Granted: November 30, 2004
Patent Number:
6826296
Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having…
Methods of genetic analysis using nucleic acid arrays
Granted: November 23, 2004
Patent Number:
6821724
The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of murine genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. As such, the invention related to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.
System, method, and user interfaces for mining of genomic data
Granted: November 9, 2004
Patent Number:
6816867
A data mining tool is described that includes a data structure populator that stores one or more first sets of data selected for querying into a first data structure. The tool also has a query builder that builds at least a first query based, at least in part, on one or more query parameters. Also included in the tool is a query manager that interrogates the first data structure with the first query. The one or more first sets of data are based, at least in part, on experiments using…
Release of intracellular material
Granted: November 2, 2004
Patent Number:
6811981
Intracellular material is released from bacterial, yeast, plant, animal, insect or human cells by the application of a low voltage such as 1 to 10 V to a suspension containing the cells. The conditions may be selected such that DNA released from the cells is electrochemically denatured so as to be available for use in an amplification procedure.
System, method, and product for dynamic noise reduction in scanning of biological materials
Granted: November 2, 2004
Patent Number:
6813567
Systems and methods are described for processing an emission signal, such as a fluorescent signal, to compensate for noise in an excitation beam, such as a laser beam. As one example, a scanning system is described that includes an excitation signal generator that provides an excitation signal having one or more representative excitation values representative of an excitation beam; an excitation reference provider that provides at least one excitation reference value; a normalization…
Methods and compositions for amplifying detectable signals in specific binding assays
Granted: October 19, 2004
Patent Number:
6806047
Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising…
Methods of enhancing functional performance of nucleic acid arrays
Granted: October 19, 2004
Patent Number:
6806361
Methods are provided for preparing nucleic acid arrays on a support. In these methods a plurality of nucleic acids are synthesized on the support and the synthesis steps are followed by drying steps in which the array is exposed to a dry atmosphere following the synthesis steps.
Methods and compositions for detecting signals in binding assays using microparticles
Granted: October 12, 2004
Patent Number:
6803196
Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the presently claimed invention provides a method of labeling a hybridized target wherein the target comprises a binding ligand. In another embodiment, the presently claimed invention provides methods of signal amplification.
System, method, and user interfaces for managing genomic data
Granted: October 12, 2004
Patent Number:
6804679
A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may…
Methods for improved array preparation
Granted: October 5, 2004
Patent Number:
6800439
Improved nucleic acid arrays are provided which have been prepared in a non-oxidizing atmosphere.
Electrode capture of nucleic acid
Granted: September 21, 2004
Patent Number:
6794130
Nucleic acid is captured from a mixture of cellular debris produced by cell lysis by exposing the mixture to an electrode and applying a nucleic acid capturing voltage to the electrode which is then removed from the mixture carrying said nucleic acid. The nucleic acid is undamaged and can be amplified by PCR.
Methods of small sample amplification
Granted: September 21, 2004
Patent Number:
6794138
The present invention relates to the amplification of nucleic acids, preferably from mRNA. A primer and promoter are added to a target sequence to be amplified and then the target is amplified in an in vitro transcription reaction and the product of this reaction is used as template for subsequent rounds of amplification.
