Abstract: Methods of preparing biopolymeric arrays are provided. The subject methods include immobilizing at least a first population of a number of copies of a first probe for a first target to a surface of a solid support, wherein the number of probe copies of the first population is dependant on the at least suspected abundance of the target in a sample for which the array is designed. Also provided are biopolymeric arrays that include at least a first population of a number of copies of a first probe for a first target immobilized on a surface of a solid support, wherein the number of probe copies is dependant on the at least suspected abundance of the target present in a sample for which the array is designed to assay. The subject invention also includes algorithms present on computer readable mediums and kits for use in practicing the subject methods.

Abstract: A method of fabricating an array of multiple chemical probes bonded to a surface of a substrate at different features of the array. The method may include depositing drops comprising a linking agent onto the surface, so that the linking agent will bind to the substrate surface. Drops comprising the chemical probes or probe precursors are deposited at the multiple feature locations, so that the probes or probe precursors bind to the linking agent at the feature locations. The foregoing step of deposition of chemical probes or probe precursors, may be repeated (with the same or different probes or probe precursors) as needed so as to form the array. Other apparatus, computer program products and methods are also provided.

Abstract: A method of fabricating one or more arrays of multiple chemical probes bound to a surface of a substrate at different features of the array. The method may include contacting each of at least ten different probes or probe precursors with different locations on the substrate surface, so that each of the probes or probe precursors binds to the different locations through the linker agent, and repeating this as needed. The one or more arrays are therefore formed with at least ten features of different probe composition which are repeated with a different probe density. Arrays, other methods, apparatus and computer program products are further provided.

Abstract: Methods of producing nucleic acid arrays using an in situ nucleic acid synthesis protocol are provided, where the in situ nucleic acid synthesis protocol includes a plurality of cycles, each of which includes: (I) a monomer attachment step; and (II) a functional group, e.g., 5′OH, generation step, the latter of which includes: (a) oxidation and (b) deblocking substeps. A feature of the subject methods is that the deblocking substep is performed by contacting a substrate surface with a deblocking solution made up of a deblocking agent present in an organic solvent, wherein the organic solvent is toluene or another organic solvent having substantially the same vapor pressure. Also provided are the arrays produced using the subject methods, as well as methods for use of the arrays and kits that include the same.

Abstract: Methods and compositions for high-throughput identification of protein/nucleic acid binding pairs are provided. In the subject methods, a nucleic acid probe array, e.g., a molecular beacon probe array, is contacted with a target nucleic acid population to produce a hybridized array. The resultant hybridized array is then contacted with a population of proteins to produce a protein bound array. Any resultant array surface bound target nucleic acid/protein complexes are then detected to identify protein/nucleic acid binding pairs. In certain embodiments, the protein and/or nucleic acid members of the identified protein/nucleic acid binding pairs are further characterized. Also provided are systems and kits for use in practicing the subject methods. The subject invention finds use in a variety of different applications.

Abstract: A method for fabricating a chemical array with multiple features. The method may include ejecting drops from an ejection head spaced from a substrate surface and during movement relative to the substrate surface, onto the substrate surface while varying an ejection velocity of the drops according to a predetermined pattern. An apparatus and computer program product which can execute such the foregoing method are also provided.

Abstract: Methods and compositions for high-throughput identification of protein/nucleic acid binding pairs are provided. In the subject methods, a nucleic acid probe array, e.g., a molecular beacon probe array, is contacted with a target nucleic acid population to produce a hybridized array. The resultant hybridized array is then contacted with a population of proteins to produce a protein bound array. Any resultant array surface bound target nucleic acid/protein complexes are then detected to identify protein/nucleic acid binding pairs. In certain embodiments, the protein and/or nucleic acid members of the identified protein/nucleic acid binding pairs are further characterized. Also provided are systems and kits for use in practicing the subject methods. The subject invention finds use in a variety of different applications.

Abstract: Apparatus and methods are disclosed for determining a functional property of a fluid in a chamber. A support to which is bound a plurality of test elements is introduced into the chamber. Each of the test elements comprises a reaction domain and a detection domain. A fluid that is interactive with the reaction domains is introduced into the chamber. Fluid is removed from the chamber. The locations at which the fluid has not interacted with the reaction domains is determined by means of the detection domains. The locations are then related to the functional property of the fluid.

Abstract: Methods and apparatus are disclosed for synthesizing a plurality of compounds such as biopolymers on the surface of supports. The synthesis comprises a plurality of steps in which reagents for conducting the synthesis are deposited on the surface of the support to form precursors of the chemical compounds and, ultimately, the chemical compounds themselves. An error in the deposition may occur in one or more of the plurality of steps. In the method in accordance with the present invention, a reagent for forming the chemical compounds is deposited on the surface of the support. A determination is made as to whether an error occurred in the depositing of the reagent. If an error is detected, then, in accordance with the present invention, the support is treated to re-deposit at least some of those reagents that were not correctly deposited because of the error in the deposition step.

Abstract: Methods are disclosed for synthesizing a plurality of compounds on the surface of supports. The synthesis comprises a series of cycles of steps in which reagents for conducting the synthesis are deposited on the surface of the support to form the chemical compounds. At least one physical parameter of the deposition varies between cycles The method comprises conducting the synthesis in at least two sets of cycles, arbitrarily designated as a first set and a second set. Each cycle comprises at least one step of depositing reagents on a surface by means of droplet dispensing elements that traverse the surface of the support. At least one, and desirably all, of the following deposition parameters are employed as indicated: The number of times of repetition for a step of depositing reagents in at least one cycle of the second set is less than the number of times of repetition for a corresponding step in at least one cycle of the first set.

Abstract: The invention provides an apparatus and method for determining a signal produced by a micro array device. The apparatus provides an unstructured probe and structured probe. The unstructured probe binds to a target and provides a first signal that can be compared to a second signal produced by a structured probe. A more accurate level of intensity of the first signal can be determined by comparing to the second signal produced by the structured probe. A method for determining a more accurate level of signal intensity produced from the unstructured probes bound to the target is also disclosed.

Abstract: Apparatus and methods are disclosed for storing a plurality of supports having a plurality of chemical compounds bound to the surfaces of the supports. In the apparatus, a mechanism for diffusively introducing pressurized gas into the apparatus is in fluid communication with an outlet element comprising a plurality of openings. A holding chamber for the supports is in fluid communication with the outlet element. The outlet element and the holding chamber are disposed such that gas flow through the chamber is substantially uniform and unidirectional. The holding chamber comprises an opening sufficient to permit movement of the supports to and from the holding chamber and comprises a plurality of holding elements for holding the supports.