Combinatorial strategies for polymer synthesis
Granted: August 25, 2005
Application Number:
20050186683
A method and device for forming large arrays of polymers on a substrate (401). According to a preferred aspect of the invention, the substrate is contacted by a channel block (407) having channels (409) therein. Selected reagents are delivered through the channels, the substrate is rotated by a rotating stage (403), and the process is repeated to form arrays of polymers on the substrate. The method may be combined with light-directed methodolgies.
System, method, and product for efficient fluid transfer using and addressable adaptor
Granted: August 18, 2005
Application Number:
20050180894
In one embodiment, an adaptor is described that comprises an interface that engages one or more components of an, instrument that introduce a fluid to the interface; a first channel that directs the fluid from the interface to a housing operatively coupled to the adaptor, where the housing comprises a chamber and a biological probe array positioned within the chamber; and a second channel that directs the fluid away from the housing.
Substrate preparation process
Granted: August 18, 2005
Application Number:
20050181396
The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
Methods for making a device for concurrently processing multiple biological chip assays
Granted: August 18, 2005
Application Number:
20050181403
Methods for concurrently processing multiple biological chip assays by providing a biological chip plate comprising a plurality of test wells, each test well having a biological chip having a molecular probe array; introducing samples into the test wells, subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a…
Methods of array synthesis
Granted: August 18, 2005
Application Number:
20050181421
Radiation-activated catalysts (RACs), autocatalytic reactions, and protective groups are employed to achieve a highly sensitive, high resolution, radiation directed combinatorial synthesis of pattern arrays of diverse polymers When irradiated, RACs produce catalysts that can react with enhancers, such as those involved in autocatalytic reactions The autocatalytic reactions produce at least one product that removes protecting groups from synthesis intermediates This invention has a wide…
Substrate preparation process
Granted: August 18, 2005
Application Number:
20050181431
The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
Single-phase amplification of nucleic acids
Granted: August 11, 2005
Application Number:
20050176054
The amplification of nucleic acids in a single phase can reliably provide products at relatively low cost and labor. A single-phase amplification can also increase the amount of nucleic acids while preserving the relative abundance of the individual nucleic acid species, or portions thereof. A single-phase amplified nucleic acid preparation may be analyzed in a gene expression monitoring system, preferably involving a nucleic acid probe array.
Guided deposition in spatial arrays
Granted: August 11, 2005
Application Number:
20050176058
An apparatus and method is provided for preparing and using a very large and diverse array of compounds on a substrate having rapidly accessible locations. The substrate contains cells in which the compounds of the array are located. Surrounding the cells is a non-wetable surface that prevents the solution in one cell from moving to adjacent cells. The compounds are delivered to the individual cells of the array by a micropipette attached to an X-Y translation stage.
Use of pooled probes in genetic analysis
Granted: August 4, 2005
Application Number:
20050170412
The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger…
Methods of screening for B cell activity modulators
Granted: August 4, 2005
Application Number:
20050169841
The invention provides for the identification of all genes, whether known or novel, which are differentially expressed within and among B cells, making possible the characterization of their temporal regulation and function in the B cell response and/or in B cell mediated disorders. Expression profiles, nucleic acids and proteins are provided for differing states of B cells, including resting, naïve, activated, tolerant and immunosuppressed B cells. The present invention makes possible…
Compositions and methods involving direct write optical lithography
Granted: August 4, 2005
Application Number:
20050169589
In one embodiment, fiber optic arrays or bundles are used as a light guide to transmit ultraviolet light to the substrate surface for photo-directed polymer synthesis Digital Micromirror Array (DMA) is used as a switching device to reflect light onto the entry side of the fiber optic array
Method of oligonucleotide synthesis
Granted: July 28, 2005
Application Number:
20050164207
Methods and kits for synthesizing a plurality of oligonucleotides are provided. Methods for providing a plurality of oligonucleotides enriched for full length oligonucleotides are provided. Truncated oligonucleotides are preferentially removed from the sample by digestion. Methods are also provided for amplification of a plurality of oligonucleotides.
Process for high-yield synthesis of standard length and long-mer nucleic acid arrays
Granted: July 28, 2005
Application Number:
20050164258
Protective groups which may be cleaved with an activatable deprotecting reagents are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments of the instant invention, the activatable deprotecting reagent is a photoacid generator and the protective groups are DMT for nucleic acids and tBOC for amino acids. This invention has a wide variety of applications and is particularly useful for the solid phase…
Methods and system for providing a polymorphism database
Granted: July 28, 2005
Application Number:
20050164270
Systems and methods for organizing information relating to study of polymorphisms. A database model is provided which interrelates information about one or more of, e.g, subjects from whom samples are extracted, primers used in extracting the DNA from the subjects, about the samples themselves, about experiments done on samples, about particular oligonucleotide probe arrays used to perform experiments, about analysis procedures performed on the samples, and about analysis results. The…
Genes differentially expressed in secretory versus proliferative endometrium
Granted: July 28, 2005
Application Number:
20050164272
The present invention compares expression profiles from matched samples to identify differential gene expression. Samples are matched according to physiological, pharmacological and/or disease state. Comparison of matched samples eliminates gene expression differences that are the result of changes in variables that are not of interest. The gene expression differences that remain can be attributed with a high degree of confidence to the unmatched variation. The gene expression…
Method for detecting chemical interactions between naturally occurring biological analyte molecures
Granted: July 28, 2005
Application Number:
20050164289
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…
Computer software for sequence selection
Granted: July 28, 2005
Application Number:
20050164290
Methods, systems and computer software products are provided for nucleic acid probe array design. In one preferred embodiment, target sequences are selected from various sources and processed for probe selection.
Method and apparatus for providing a bioinformatics database
Granted: July 21, 2005
Application Number:
20050157915
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.
Surface-bound, unimolecular, double-stranded DNA
Granted: July 21, 2005
Application Number:
20050158744
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…
Expression monitoring by hybridization to high density oligonucleotide arrays
Granted: July 21, 2005
Application Number:
20050158746
This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic…
