Abstract: A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.

Abstract: Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Abstract: Methods and devices for producing a nucleic acid arrays using in situ nucleic acid array synthesis protocols are provided. A feature of certain embodiments of the invention is that control probes are produced in collections of features, e.g., columns, of the arrays that have been selected according to a particular efficient control probe feature/column selection protocol. A feature of certain other embodiments of the invention is that an “all-bases-all-layers” probe set is produced in at least one of column of the arrays. Also provided are devices configured for use in the subject methods, as well as arrays produced using the subject methods and devices as well as methods for using such arrays.

Abstract: A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.

Abstract: Methods and apparatus are disclosed for synthesizing a plurality of biopolymers at predetermined feature locations on a surface of a substrate. One or more of the feature locations comprises degenerate biopolymers. One or more biopolymer subunit precursors are added, in multiple rounds of subunit additions, at each of multiple feature locations on the surface to form the plurality of biopolymers on the surface. For each feature location comprising degenerate biopolymers, the biopolymer subunit precursors comprise a mixture of biopolymer subunit precursors for forming the degenerate biopolymers at the feature location.

Abstract: A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.

Abstract: Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.

Abstract: Methods, reagents and kits are disclosed for selecting target-specific oligonucleotide probes, which may be used in analyzing a target nucleic acid sequence. In one aspect the present invention is directed to selecting a set of target-specific oligonucleotide probes. A cross-hybridization oligonucleotide probe is identified based on a candidate target-specific oligonucleotide probe for the target nucleic acid sequence. The cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event having a predetermined probability. Cross-hybridization results are determined employing the cross-hybridization oligonucleotide probe and the target-specific oligonucleotide probe. The target-specific oligonucleotide probe is selected or rejected for the set based on the cross-hybridization results.

Abstract: A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.

Abstract: A method and system for quantifying and correcting spatial-intensity trends for each channel of a microarray data set having one or more channels. The method and system of one embodiment of the present invention selects a set of features from each channel of the microarray data set. Based on the selected set of features, a surface is used to determine the intensities for all features in each channel of the microarray data set. Spatial-intensity trends within the microarray data set are quantified, based on the surface to the intensities for each channel of the microarray data set. After the surface has been determined, the spatial-intensity trend can be removed from the microarray data set.

Abstract: The invention provides a composition, kit and method for hybridizing a probe and target at a temperature lower than their standard hybridization temperature. The chemical component added to the composition has a formula R(NH2)C?O, where R is amino or alkyl. A method for use of the chemical component and composition is also disclosed.

Abstract: The invention provides a composition, kit and method for hybridizing a probe and target at a temperature lower than their standard hybridization temperature. The chemical component added to the composition has a formula R(NH2)C?O, where R is amino or alkyl. A method for use of the chemical component and composition is also disclosed.

Abstract: Methods for substantially improved detection and analysis in nucleic acid hybridization assays are described. The methods provide the reliable estimation of background signal which derives primarily from nonspecific hybridization. The invention is useful in chemical, biological, medical and diagnostic techniques, as well as for drug discovery.

Abstract: Nucleic acid arrays that have background features, and methods for using the same, are provided. The subject nucleic acid arrays include both hybridization features and background features, where the background features provide a background signal in a hybridization assay that is made up of a feature substrate component, a nucleic acid probe component and a nucleic acid probe non-specific binding component. In practicing the subject methods, the arrays are contacted with a sample and signals are observed for both hybridization features and background features. The background feature signal is then subtracted from the hybridization feature signal to obtain a background corrected hybridization feature signal that is employed as the output of the assay, e.g., to determine the presence, either qualitatively or quantitatively, of the analyte target nucleic acid in the sample. Also provided are kits for use in practicing the subject methods.

Abstract: A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

Abstract: A polynucleotide array, and methods of making and using such arrays. The array may include a first set of multiple features each of which has first polynucleotide molecules of at least 400 nucleotides in length, and a second set of features each of which has second polynucleotide molecules of no more than 100 nucleotides in length. The second set of features can be used as control features, or to replace failed sequences in an enzymatic amplification to produce first polynucleotides, or to detect polymorphisms or splice variants which may not be detected by a particular first polynucleotide.

Abstract: A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.

Abstract: An apparatus and method for separating and identifying chemical moieties. The apparatus employs a micro array device coupled to a detector such as a mass spectrometer system. The apparatus both separates and identifies target molecules without the requirement of extraneous tags or fluorescent markers. Methods for using the apparatus are also disclosed.

Abstract: Array-based clinical assays and compositions for use in practicing the same are provided. A feature of the subject array-based clinical assays is that they include a sample quality evaluation step that is independent from the clinical assay step of the assays, where the sample quality evaluation step may be performed in a number of different ways. Also provided are compositions, devices and kits for use in practicing the subject methods.

Abstract: Methods and devices for producing a nucleic acid arrays using in situ nucleic acid array synthesis protocols are provided. A feature of certain embodiments of the invention is that control probes are produced in collections of features, e.g., columns, of the arrays that have been selected according to a particular efficient control probe feature/column selection protocol. A feature of certain other embodiments of the invention is that an “all-bases-all-layers” probe set is produced in at least one of column of the arrays. Also provided are devices configured for use in the subject methods, as well as arrays produced using the subject methods and devices as well as methods for using such arrays.