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: 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 of fabricating polynucleotide arrays includes dissolving a nucleotide monomer, oligonucleotide, or polynucleotide in a solvent containing ionic liquid and depositing the resulting solution on an array substrate. The method has particular application to fabrication of an addressable array of polynucleotides on a substrate that carries substrate bound moieties each with a hydroxyl group. The process may be repeated at specific locations on the array to elongate the polynucleotide deposited on the array.

Abstract: A method of synthesizing polynucleotides is disclosed. The method involves contacting a first nucleotide with a selected reactive group in the presence of an ionic liquid. The selected reactive group may be on a second nucleotide, a polynucleotide, or on a moiety on an insoluble substrate, for example in an oligonucleotide synthesizer.

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 and compositions for modifying a substrate surface are provided. In accordance with the subject methods, a substrate surface is contacted with a particulate-containing fluid. The fluid is then ultrasonically or sonically agitated to modify the substrate surface. In certain embodiments, the particulate-containing fluid has a pH above the isoelectric point of the substrate. Also provided are devices capable of providing ultrasonic and/or sonic energy and which include a non-acidic, particulate-containing fluid. The subject invention also provides systems and kits for use in practicing the subject methods.

Abstract: The invention provides a method and apparatus for micro array fabrication exclusive from the impact of a gas. A housing with a gas free chamber provides for improved micro array fabrication with a lower defect rate. The invention provides a housing that excludes a gas such as ozone to prevent interaction with probe construction or attachment. A method of fabricating a micro array in an ozone free environment is also disclosed.

Abstract: A method for specifically and uniformly synthesizing desired polymers within molecular array elements. Droplets containing a reactive monomer are successively applied to the elements of a molecular array in order to synthesize a substrate-bound polymer. Application of an initial droplet, having a first volume, defines the position and size of a molecular array element. Subsequent droplets are applied, to add successive reactive monomers to growing nascent polymers within the molecular array element, with covering volumes so that, even when application of the subsequent droplets is misregistered, the entire surfaces of the elements of the molecular array are exposed to the subsequently applied droplets. Following application of initial droplets, the surface of the molecular array is exposed to a solution containing a very efficient capping agent in order to chemically cap any unreacted nascent growing polymers and any unreacted substrate molecules.

Abstract: A method of fabricating an addressable array of biopolymers on a substrate using a biomonomer with a first linking group which must be activated for linking to a substrate bound moiety, and apparatus and computer program products for executing the method. The method includes forming on a region of the substrate carrying the substrate bound moiety, a solid activator composition. A biomonomer containing fluid composition is deposited on the region so that the solid activator activates the first linking group and the biomonomer links to the substrate bound moiety. The foregoing steps may be repeated, wherein a biomonomer deposited and linked to the substrate bound moiety in one cycle is the substrate bound moiety for the next cycle, so as to form the biopolymer.

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: A method of fabricating polynucleotide arrays includes dissolving a nucleotide monomer, oligonucleotide, or polynucleotide in a solvent containing ionic liquid and depositing the resulting solution on an array substrate. The method has particular application to fabrication of an addressable array of polynucleotides on a substrate that carries substrate bound moieties each with a hydroxyl group. The process may be repeated at specific locations on the array to elongate the polynucleotide deposited on the array.

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 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: 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: 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: A method including coupling the moiety to a phospho or phosphite derivative of a protected alcohol, so as to form the corresponding phosphate or phosphite between the hydroxy and phospho or phosphite groups. The hydroxy group may be later de-protected by hydrolyzing the resulting compound to deprotect the protected alcohol and cleave the phosphate from the moiety so as to regenerate the hydroxy group of the moiety. The method has particular application to fabrication of addressable polynucleotide arrays and allows failed sequences, as well as inter-feature regions, to be left with a free hydroxy group at the ends of the molecules (failed sequences or linkers) at such locations.

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: 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: A method for specifically and uniformly synthesizing desired polymers within molecular array elements. Droplets containing a reactive monomer are successively applied to the elements of a molecular array in order to synthesize a substrate-bound polymer. Application of an initial droplet, having a first volume, defines the position and size of a molecular array element. Subsequent droplets are applied, to add successive reactive monomers to growing nascent polymers within the molecular array element, with covering volumes so that, even when application of the subsequent droplets is misregistered, the entire surfaces of the elements of the molecular array are exposed to the subsequently applied droplets. Following application of initial droplets, the surface of the molecular array is exposed to a solution containing a very efficient capping agent in order to chemically cap any unreacted nascent growing polymers and any unreacted substrate molecules.