Bioarray chip reaction apparatus and its manufacture
Granted: January 6, 2005
Application Number:
20050003421
A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
Nucleic acid labeling compounds
Granted: January 6, 2005
Application Number:
20050003496
Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. Methods for making such heterocyclic compounds are also disclosed. The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
Method, system, and computer software for providing a genomic web portal
Granted: January 6, 2005
Application Number:
20050004768
Systems, methods, and computer program products are described that process inquiries or orders regarding purchase of biological devices, substances, or related reagents. In some implementations, a user selects probe-set identifiers that identify microarray probe sets capable of enabling detection of biological molecules. Corresponding genes or EST's are identified and are correlated with related product data, which is provided to the user. Further, the user may select products for…
Methods of small sample amplification
Granted: January 6, 2005
Application Number:
20050003392
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. Polyadenylated control transcripts are added to the nucleic acid sample prior to the first step of amplification to monitor the efficiency of the amplification and…
Method of manufacturing
Granted: December 30, 2004
Application Number:
20040265838
A method of manufacturing items in parallel. Selected samples of items to be manufactured are subjected to additional steps in a manufacturing process. If such sample items meet the requisite quality control standard, remaining items are subjected to further manufacturing steps. If the sample items which have been further processed do not meet the requisite quality control standard, the lot from which the samples do not undergo the additional manufacturing step. Invention provides an…
Capturing sequences adjacent to type-IIs restriction sites for genomic library mapping
Granted: December 30, 2004
Application Number:
20040265842
The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
Methods for oligonucleotide probe design
Granted: December 23, 2004
Application Number:
20040259124
The present invention includes methods for predicting the quantitative response of probes on a microarray. In a preferred embodiment, sequence dependent parameters are predicted and then used to predict probe response.
Thermal and fluidic cycling device for nucleic acid hybridization
Granted: December 16, 2004
Application Number:
20040253714
In accordance with various embodiments of the invention, an apparatus is provided for hybridizing a nucleic acid microarray immobilized on a surface of a solid substrate. The apparatus comprises at least one assembly for securing the solid substrate during hybridization, the assembly comprising a carrier and a cover having a surface facing the carrier. The carrier and the cover can be dimensioned to receive the solid substrate between the carrier and the surface of the cover so that the…
Iterative resequencing
Granted: December 9, 2004
Application Number:
20040248176
The invention provides iterative methods of analyzing a target nucleic acid that represents a variant of a reference nucleic acid. An array of probes is designed to be complementary to an estimated sequence of a target nucleic acid. The array of probes is then hybridized to the target nucleic acid. The target sequence is reestimated from hybridization pattern of the array to the target nucleic acid. A further array of probes is then designed to be complementary to the reestimated…
Releasable polymer arrays
Granted: December 9, 2004
Application Number:
20040248162
Methods are provided for fabricating an array of polymers wherein the polymers may be released from the surface of the array by activation of a cleavable moiety. Also provided are arrays of polymers having of polymers wherein the polymers can be released from the surface of the array by activation of a releasable group. Arrays of nucleic acids wherein a nucleic acid probe may be released from the array by activation of a releasable groups and methods for fabrication of such arrays are…
Arrays for detecting nucleic acids
Granted: December 9, 2004
Application Number:
20040248147
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.
Photoactivateable silane compounds and methods for their synthesis and use
Granted: November 25, 2004
Application Number:
20040234788
In one aspect of the invention, photoactivatable silane compounds and methods for their synthesis and use are provided. In one embodiment, the photoactivatable silane compounds synthesized are represented by a formula: PG-LS-SN, wherein PG is a photoactivatable group, LS is a linkage and spacer group, and SN is a silane group. The silanes allow the photoactivatable silane compounds to be covalently bound to the surface of a substrate such as silica. The photoactivatable group forms a…
Methods for reducing background on polynucleotide arrays
Granted: November 25, 2004
Application Number:
20040234964
Methods are provided for reducing background signal associated with hybridization of nucleic acid arrays to nucleic acid samples, the method comprising hybridizing the array to the sample in the presence of a poly-anionic polymer (PAP). Background associated with hybridization of arrays to samples interferes with signal generated by specific binding to the probe array un-desirably lowers the signal to noise ratio (SNR) and generates an overall loss of sensitivity for nucleic acid arrays.
Methods and compositions for profiling transcriptionally active sites of the genome
Granted: November 25, 2004
Application Number:
20040235008
In some embodiments of the invention, methods are provided to profile transcriptionally active sites of the genome. The methods employ hybridization of a large number of oligonucleotide probes to nucleic acid derivatives of cytosolic RNAs derived from cell lines that respond to an exogenous stimulation.
Guided deposition in spatial arrays
Granted: November 25, 2004
Application Number:
20040235033
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.
System, method, and encased probe array product
Granted: November 25, 2004
Application Number:
20040235147
In one embodiment an encased probe array is described. The encased probe array comprises a first layer including one more active areas disposed thereon, where each of the one or more active areas includes a plurality of probes each enabled to hybridize a biological molecule; one or more second layers attached to the first layer; and one or more chambers formed from at least one of the one or more second layers, where each of the one or more active areas is associated with at least one of…
System and method for calibration and focusing a scanner instrument using elements associated with a biological probe array
Granted: November 11, 2004
Application Number:
20040224332
A system is described for providing focus elements associated with a biological probe array that comprises a biological probe array enabled to hybridize target molecules to probes disposed in an active area of the biological probe array; and focus elements disposed on the biological probe array, where the focus elements represent an unambiguous pattern.
System, method, and computer software product for instrument control and data acquisition, analysis, management and storage
Granted: November 4, 2004
Application Number:
20040220897
A system is described for providing an interface enabled to transfer data between databases that comprises a database that stores data and is associated with a computer workstation, where the data includes data associated with biological probe arrays; a second database that stores the data that is associated with a server; and an interface that transfers the data between the databases based, at least in part, upon a user selection.
Method of cRNA synthesis
Granted: October 28, 2004
Application Number:
20040214210
Copy or antisense RNA is synthesized in a way that preserves the relative amounts of particular RNA molecules in a population. RNA is reverse transcribed to form first strand cDNA. Second strand cDNA is made by enzyme-catalyzed DNA synthesis using exogenous primers, preferably random primers. Double-stranded cDNA formed from the first and second strands is then used as a template for in vitro transcription to form copy or antisense RNA. The transcription is driven by a promoter sequence…
System, method and product for providing a stable calibration standard for optical systems
Granted: October 14, 2004
Application Number:
20040201844
A system is described for providing a wavelength of light that comprises: a scanner that provides a first wavelength; and an optical assembly that emits a second wavelength based, at least in part upon the first wavelength, wherein the second wavelength is not the result of a fluorescent emission.
