Abstract: Methods, apparatus, and computer program products to form arrays of polymers each having a pattern of features on a surface of a flexible elongated web, comprising. In a method polymers or their precursor units are applied at an application station to the surface. Multiple features are covered at a reagent station with a continuous volume of reagent which chemically reacts with precursors or the web. The flexible elongated web is driven in a lengthwise direction through the application station. This sequence may be repeated as needed to form the arrays along the web. Also provided is a method preparing a surface of a flexible elongated web to receive a biopolymer array.

Abstract: A method and apparatus for using arrays of polymers each having a pattern of features over a corresponding array region on a surface of a flexible elongated web. In this method each array region may be exposed to a corresponding continuous volume of a sample fluid. A method and apparatus are also provided for reading arrays disposed along a surface of a flexible elongated web. In one such method the web with the arrays thereon may be transported in a lengthwise direction past a reading location at which a characteristic of the features is read, while restraining the web on both surfaces on either side of the reading location to assist in maintaining the reading location flat.

Abstract: Calibration devices for optical scanners and methods for their use are provided. The subject devices are characterized by having a polymeric coating with at least one fluorescent agent, where the devices have minimal local and global nonuniformities. The subject device may also include one or more photobleached regions. In using the subject devices, a surface is illuminated with at least one light source, fluorescence data is obtained from the surface and the optical system is calibrated based upon the obtained fluorescence data. The subject invention finds use in a variety of optical scanners, including biopolymeric array optical scanners. Also provided are kits for use in verifying and calibrating optical scanners.

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: Methods for stably associating a polyelectrolyte coating or film to a substrate surface, as well as the coated substrates produced thereby, are disclosed herein. In the subject methods, substrate surfaces are coated with a polyelectrolyte, and the coated substrate surfaces are treated with a bifunctional molecule under conditions sufficient to stably associate the film to the array surface. The subject methods find use in a variety of different applications, including the production of mircoarrarys.

Abstract: The invention provides a solid support for adsorbing a biomolecule. The support comprises a surface coating having a non-nucleotidic polymer tethered to a surface reactive site. The polymer comprises a backbone, terminus, and adsorbing moieties covalently attached to the backbone and capable of adsorbing a biomolecule that can assume a plurality of conformations. The polymer is generally tethered to the surface at its terminus and the backbone exhibits sufficient mobility and flexibility such that a biomolecule adsorbed by the adsorbing moieties can assume a desired conformation for hybridization. Also provided is a process for preparing a surface coating having a functionalized surface.

Abstract: A method of fabricating an array of biopolymers provides a shield for biochemical reactions and biochemical reactants and is particularly useful for those reactions and reactants that are susceptible to reaction with a component of the ambient environment during the fabrication of the array. The method is applicable to the conventional fabrication and synthesis methods used to fabricate a biopolymer array, such as in situ synthesis of biopolymers on an array and the attachment of pre-synthesized biopolymers on to an array. The method comprises applying a non-miscible fluid (NMF) to the array surface where the biopolymers are being synthesized or attached. The NMF is inert and insoluble with the biochemical reactants and other ancillary materials in solution used in conventional synthesis or attachment of biopolymers.

Abstract: Methods, apparatus, and computer program products to form arrays of polymers each having a pattern of features on a surface of a flexible elongated web, comprising. In a method polymers or their precursor units are applied at an application station to the surface. Multiple features are covered at a reagent station with a continuous volume of reagent which chemically reacts with precursors or the web. The flexible elongated web is driven in a lengthwise direction through the application station. This sequence may be repeated as needed to form the arrays along the web. Also provided is a method preparing a surface of a flexible elongated web to receive a biopolymer array.

Abstract: Calibration devices for optical scanners and methods for their use are provided. The subject devices are characterized by having a polymeric coating with at least one fluorescent agent, where the devices have minimal local and global nonuniformities. The subject device may also include one or more photobleached regions. In using the subject devices, a surface is illuminated with at least one light source, fluorescence data is obtained from the surface and the optical system is calibrated based upon the obtained fluorescence data. The subject invention finds use in a variety of optical scanners, including biopolymeric array optical scanners. Also provided are kits for use in verifying and calibrating optical scanners.

Abstract: A buffer composition, method and kit for hybridizing microarrays of nucleic acids bound to an adsorbed polymer surface of a siliceous substrate provide an envelope of conditions to hybridize nucleic acid targets, while preserving theintactness of the adsorbed polymer surface of the array. The buffer composition comprises a non-chelating buffering agent, a pH within a range of pH 6.4 and 7.5, a monovalent cation having a monovalent cation concentration that ranges from about 0.01 M to about 2.0 M, and optionally relatively lower concentrations of a chelating agent and an ionic surfactant. The total cation concentration of the buffer composition ranges from about 0.02 M to about 2.0 M. The method comprises incubating the targets with the microarray in the buffer composition at a temperature between about 55° C. and 70° C.

Abstract: An array assembly and a method of fabricating such an assembly. The array assembly may include a plastic base layer, a glass layer forward of the base layer, and an array of polymers having a pattern of features on a front surface of the glass layer. A method of reading an array is also provided in which the array has a plastic base layer, a glass layer forward of the base layer, a reflective layer intermediate the base and glass layers, and an array on a front surface of the glass layer. The method may include illuminating features of the array and detecting any resulting fluorescence.

Abstract: Calibration devices for optical scanners and methods for their use are provided. The subject devices are characterized by having a polymeric coating with at least one fluorescent agent, where the devices have minimal local and global nonuniformities. The subject device may also include one or more photobleached regions. In using the subject devices, a surface is illuminated with at least one light source, fluorescence data is obtained from the surface and the optical system is calibrated based upon the obtained fluorescence data. The subject invention finds use in a variety of optical scanners, including biopolymeric array optical scanners. Also provided are kits for use in verifying and calibrating optical scanners.

Abstract: The invention provides a solid support for adsorbing a biomolecule. The support comprises a surface coating having a non-nucleotidic polymer tethered to a surface reactive site. The polymer comprises a backbone, terminus, and adsorbing moieties covalently attached to the backbone and capable of adsorbing a biomolecule that can assume a plurality of conformations. The polymer is generally tethered to the surface at its terminus and the backbone exhibits sufficient mobility and flexibility such that a biomolecule adsorbed by the adsorbing moieties can assume a desired conformation for hybridization. Also provided is a process for preparing a surface coating having a functionalized surface.

Abstract: A method and apparatus for using arrays of polymers each having a pattern of features over a corresponding array region on a surface of a flexible elongated web. In this method each array region may be exposed to a corresponding continuous volume of a sample fluid. A method and apparatus are also provided for reading arrays disposed along a surface of a flexible elongated web. In one such method the web with the arrays thereon may be transported in a lengthwise direction past a reading location at which a characteristic of the features is read, while restraining the web on both surfaces on either side of the reading location to assist in maintaining the reading location flat.

Abstract: Methods, apparatus, and computer program products to form arrays of polymers each having a pattern of features on a surface of a flexible elongated web, comprising. In a method polymers or their precursor units are applied at an application station to the surface. Multiple features are covered at a reagent station with a continuous volume of reagent which chemically reacts with precursors or the web. The flexible elongated web is driven in a lengthwise direction through the application station. This sequence may be repeated as needed to form the arrays along the web. Also provided is a method preparing a surface of a flexible elongated web to receive a biopolymer array.

Abstract: Methods of producing ligand arrays, e.g., polypeptide and nucleic acid arrays, as well as the arrays produced thereby, methods for use of the arrays and kits that include the same, are provided. In the subject methods, a substrate having a surface displaying olefinic functional groups, e.g., olefin groups having a single site of unsaturation, are modified such that the olefinic functional groups are converted to ligand reactive functional groups. The resultant substrate is then contacted with ligands, e.g., via deposition of each different ligand onto a different region of the surface, resulting in covalent attachment of the contacted ligand to the surface via reaction with the ligand reactive functional groups. Ligand arrays produced via the subject methods demonstrate a number of desirable properties, e.g., nucleic acid arrays produced by the subject methods provide high signal intensity with low background in nucleic acid hybridization assays, etc.

Abstract: A buffer composition, method and kit for hybridizing microarrays of nucleic acids bound to an adsorbed polymer surface of a siliceous substrate provide an envelope of conditions to hybridize nucleic acid targets, while preserving the intactness of the adsorbed polymer surface of the array. The buffer composition comprises a non-chelating buffering agent, a pH within a range of pH 6.4 and 7.5, a monovalent cation having a monovalent cation concentration that ranges from about 0.01 M to about 2.0 M, and optionally relatively lower concentrations of a chelating agent and an ionic surfactant. The total cation concentration of the buffer composition ranges from about 0.02 M to about 2.0 M. The method comprises incubating the targets with the microarray in the buffer composition at a temperature between about 55° C. and 70° C.

Abstract: Methods for stably associating a polyelectrolyte coating or film to a substrate surface, as well as the coated substrates produced thereby, are disclosed herein. In the subject methods, substrate surfaces are coated with a polyelectrolyte, and the coated substrate surfaces are treated with a bifunctional molecule under conditions sufficient to stably associate the film to the array surface. The subject methods find use in a variety of different applications, including the production of mircoarrarys.

Abstract: Low surface energy functionalized surfaces on solid supports are provided by treating a solid support having hydrophilic moieties on its surface with a derivatizing composition containing a mixture of silanes. A first silane provides the desired reduction in surface energy, while the second silane enables functionalization with molecular moieties of interest, such as small molecules, initial monomers to be used in the solid phase synthesis of oligomers, or intact oligomers. Molecular moieties of interest may be attached through cleavable sites. Derivatizing compositions for carrying out the surface functionalization process are provided as well.

Abstract: A method of fabricating an array of biopolymers provides a shield for biochemical reactions and biochemical reactants and is particularly useful for those reactions and reactants that are susceptible to reaction with a component of the ambient environment during the fabrication of the array. The method is applicable to the conventional fabrication and synthesis methods used to fabricate a biopolymer array, such as in situ synthesis of biopolymers on an array and the attachment of pre-synthesized biopolymers on to an array. The method comprises applying a non-miscible fluid (NMF) to the array surface where the biopolymers are being synthesized or attached. The NMF is inert and insoluble with the biochemical reactants and other ancillary materials in solution used in conventional synthesis or attachment of biopolymers.