Nucleic acid arrays
Granted: July 17, 2001
Patent Number:
6261776
A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection…
Functionalized silicon compounds and methods for their synthesis and use
Granted: July 17, 2001
Patent Number:
6262216
Provided are functionalized silicon compounds and methods for their synthesis and use. The functionalized silicon compounds include at least one activated silicon group and at least one derivatizable functional group. Exemplary derivatizable functional groups include hydroxyl, amino, carboxyl and thiol, as well as modified forms thereof, such as activated or protected forms. The functionalized silicon compounds may be covalently attached to surfaces to form functionalized surfaces which…
Process for microfabrication of an integrated PCR-CE device and products produced by the same
Granted: July 17, 2001
Patent Number:
6261431
A fully integrated monolithic small volume PCR-CE device in glass, or the like materials, is fabricated using thin film metal heaters and thermocouples to thermally cycle sub-microliter PCR volumes. Successful amplification of a PCR fragment is demonstrated on a PCR-CE chip. The process utilizes a linear polyacrylamide surface coating coupled with addition of BSA to the amplification buffer was necessary to obtain amplification efficiencies comparable to a positive control. The…
Method and apparatus for imaging a sample on a device
Granted: June 26, 2001
Patent Number:
6252236
A method and apparatus for imaging a sample are provided. An electromagnetic radiation source generates excitation radiation which is sized by excitation optics to a line. The line is directed at a sample resting on a support and excites a plurality of regions on the sample. Collection optics collect response radiation reflected from the sample I and image the reflected radiation. A detector senses the reflected radiation and is positioned to permit discrimination between radiation…
Computer-aided visualization and analysis system for sequence evaluation
Granted: June 5, 2001
Patent Number:
6242180
A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816)…
Methods for testing oligonucleotide arrays
Granted: May 29, 2001
Patent Number:
6238862
Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acids.
Printing molecular library arrays
Granted: May 29, 2001
Patent Number:
6239273
A method and apparatus for selectively applying a print material onto a substrate for the synthesis of an array of oligonucleotides at selected regions of a substrate. The print material includes a barrier material, a monomer sequence, a nucleoside, a deprotection agent, a carrier material, among other materials. The method and apparatus also relies upon standard DMT based chemistry, and a vapor phase deprotection agent such as solid TCA and the like.
Chip-based species identification and phenotypic characterization of microorganisms
Granted: May 8, 2001
Patent Number:
6228575
This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.
Computer-aided probability base calling for arrays of nucleic acid probes on chips
Granted: May 8, 2001
Patent Number:
6228593
A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.
Method and apparatus for providing a bioinformatics database
Granted: May 8, 2001
Patent Number:
6229911
System and method for organizing information relating to polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc. The model is readily translatable into database languages such as SQL. The database model scales to permit mass processing of probe array chips.
Signal detection methods and apparatus
Granted: May 1, 2001
Patent Number:
6225625
A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection…
Polymorphism detection utilizing clustering analysis
Granted: April 24, 2001
Patent Number:
6223127
Systems and methods for detecting differences in sample polymers, such as nucleic acid sequences, are provided. Hybridization affinity information for the sample polymers is clustered so that the differences, if any, between or among the sample polymers can be readily identified. By clustering the hybridization affinity information of the sample polymers, differences in the sample polymers can be accurately achieved even in the presence of random and systematic errors.
System and methods for detection of labeled materials
Granted: March 27, 2001
Patent Number:
6207960
Labeled targets on a support synthesized with polymer sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, can be detected by exposing marked regions of sample to radiation from a source and detecting the emission therefrom, and repeating the steps of exposition and detection until the sample is completely examined.
Method for detecting chemical interactions between naturally occurring bio-polymers which are non-identical binding partners
Granted: March 20, 2001
Patent Number:
6203983
A method of using micromechanical devices as sensors for detecting chemical interactions between naturally occurring bio-polymers which are non-identical binding partners is provided. The method is useful whether the reactions occur through electrostatic forces or other forces. Induced stress, heat, or change in mass is detected where a binding partner is placed on a cantilever for possible reaction with an analyte molecules (i.e., a non-identical binding partner). The method is…
Methods and compositions for amplifying detectable signals in specific binding assays
Granted: March 20, 2001
Patent Number:
6203989
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…
Method of detecting nucleic acids
Granted: March 6, 2001
Patent Number:
6197506
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Electrochemical denaturation and annealing of nucleic acid
Granted: March 6, 2001
Patent Number:
6197508
A process is described for denaturing native double-stranded nucleic acid material into its individual strands in an electrochemical cell. The process disclosed is an electrical treatment of the nucleic acid with a voltage applied to the nucleic acid material by an electrode. The process may also employ a promoter compound such as methyl viologen to speed denaturation. The process may be used in the detection of nucleic acid by hybridizing with a labelled probe or in the amplification of…
Integrated nucleic acid diagnostic device
Granted: March 6, 2001
Patent Number:
6197595
The present invention provides a miniaturized integrated nucleic acid diagnostic device and system. The device of the invention is generally capable of performing one 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…
Method and system for providing a probe array chip design database
Granted: February 13, 2001
Patent Number:
6188783
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…
Method and apparatus for providing and expression data mining database
Granted: February 6, 2001
Patent Number:
6185561
According to the invention, a system and method for organizing expression information in a way that facilitates data mining. A database model is provided which may organize information relating to, e.g., sample preparation, expression analysis of experiment results, and intermediate and final results of mining expression and concentration results. The model is readily translatable into database languages such as SQL and the like. The database model scales to permit mining of expression…
