Abstract: Inkjet printhead solvents and methods of forming an addressable nucleotide array are disclosed.

Abstract: A method of uniformly draining liquid from a patterned surface using a flow cell is provided. The method may be employed in a variety of applications, including in chemical array fabrication. In an exemplary embodiment, the invention provides an apparatus for fabricating a chemical array that employs a flow cell. Methods of fabricating a chemical array that employ the subject apparatus and drainage methods are also provided. Also provided are the arrays produced using the subject methods, as well as methods for using those arrays.

Abstract: Methods for fabricating chemical arrays are provided. Aspects of the invention include methods for providing solid activator in feature locations of a substrate surface. Aspects of the invention also include substrates having solid activator present in feature locations thereof, arrays produced from the substrates, methods for use of the arrays and kits that include the arrays.

Abstract: Methods and apparatus are disclosed for preparing an array of polymeric compounds on a substrate. Drops of polymer subunits are dispensed to a surface of a substrate from two or more drop dispensing modules wherein each module comprises dispensers for dispensing a respective polymer-forming reagent. At least two of the modules and a substrate are brought into drop dispensing relationship in at least one step prior to conducting the step of preparing the surface for repeating the drop-dispensing step. Next, the surface is subjected to reagents to prepare the surface for repeating the drop-dispensing step. The above steps are repeated for a sufficient number of cycles to prepare the array of polymeric compounds.

Abstract: Methods and devices for producing chemical arrays are provided. Aspects of methods include employing a dedicated wash fluid reaction chamber. In certain embodiments, aspects include contacting a surface with at least a deblocking reagent to produce a deblocked surface, washing the deblocked surface in a dedicated wash fluid reaction chamber, e.g., flow cell, and then contacting the washed surface with one or more reactive moieties in a spatially controlled manner. Also provided are devices configured for use in practicing the subject methods.

Abstract: Flow cell devices and methods for using the devices are disclosed. In one aspect, the flow cell devices are used to expose substrate surfaces comprising biopolymers or monomers to a desired fluid. Workstations are also provided including a flow cell device and one or more station(s) for processing a substrate, such as one or more of a printer, reaction chamber, wash chamber, and scanner. Computer program products for implementing functions of the devices and workstations and for performing the methods are also disclosed.

Abstract: There are disclosed systems and methods in which a liquid dispensing head is positioned above the contact area of the device under test (DUT). A stream of liquid is dispensed from the head such that a continuous column of liquid extends from the head to the contact area of the test device. This column of liquid completes a circuit which allows current to flow thereby allowing for current measurement.

Abstract: Methods of producing nucleic acid arrays using an in situ nucleic acid synthesis protocol are provided. Embodiments include a functional group generation step performed by flowing a plurality of different fluids across the surface of a substrate in a manner such that any given lower density fluid is always above any given higher density fluid of the plurality. Also provided are the arrays produced using the subject methods, methods for use of the arrays, and devices for use in practicing the subject methods.

Abstract: A method, a system, and a computer-readable medium storing a program for determining array quality during in-situ manufacturing of an array includes determining an average feature coverage fraction of the array, determining a background area fraction of the array, measuring a contact angle of the background, and determining the array quality based upon the measured, feature contact angle.

Abstract: Methods of producing nucleic acid molecules using an in situ nucleic acid synthesis protocol are provided. The method can comprise contacting a substrate comprising an attached blocked nucleoside monomer or polymer with a deblocking fluid to remove the blocking group, thereby generating an unblocked attached nucleoside monomer or polymer; displacing the deblocking fluid from the substrate surface comprising the attached unblocked nucleoside monomer or polymer with a purging fluid; and reacting the attached unblocked nucleoside monomer or polymer with another blocked nucleoside monomer. Nucleic acid molecules produced by the methods are also provided and can be attached to or released from the substrate (e.g., provided in solution or in a lyophilized form).

Abstract: The invention provides methods for manufacturing a chemical array reader calibration device. Embodiments include dispensing a volume of fluorescent dye coating composition from a pulse jet fluid deposition device onto a surface of a substrate to coat the surface with the fluorescent dye coating composition. Also provided are chemical array reader calibration devices and methods of using the subject chemical array reader calibration devices to calibrate a chemical array reader. Also provided are kits that include a chemical array reader calibration device.

Abstract: The subject invention provides methods and devices for fabricating chemical arrays. Also provided are chemical arrays fabricated according to the subject methods, and methods of using chemical arrays produced according to the subject invention.

Abstract: Inkjet printhead solvents and methods of forming an addressable nucleotide array are disclosed.

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: Methods and devices for fabricating a chemical array are provided. Embodiments include determining a chemical array layout in which each feature in the layout has a size that is chosen based on its composition and fabricating a chemical array according to the chemical array layout. In certain embodiments, at least two features of an array fabricated according to the subject methods are of different sizes. Embodiments also include chemical arrays having features of different sizes, e.g., fabricated according to the subject methods. Also provided are embodiments that include fluid deposition devices capable of fabricating chemical arrays having features of different sizes, e.g., for use in practicing the subject methods. Algorithms present on computer readable mediums for use in practicing the subject methods may also be provided in certain embodiments. Embodiments of the subject invention may also include systems and kits for use in practicing the subject methods.

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 generation step, the latter of which may include: (a) oxidation and (b) deblocking substeps, and optionally a capping substep. A feature of the subject methods is that, following deblock of the surface, the deblocking fluid is displaced or purged from the surface using a fluid of different density, e.g., an oxidization fluid or wash fluid. 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 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 generation step. A feature of the subject methods is that the functional group generation step is performed by sequentially flowing a plurality of different fluids across the surface of a substrate in a manner such that the surface is not contacted with a with a triple phase interface line. 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: A generalized printhead control model is provided herein as a basis for configuring printhead control software that will operate any selected printhead or group of printheads. The subject model covers a hierarchy of classes for the attributes of software that controls the printheads in a system, such as for producing a biopolymer array.

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 generation step, the latter of which may include: (a) oxidation and (b) deblocking substeps, and optionally a capping substep. A feature of the subject methods is that, following deblock of the surface, the deblocking fluid is displaced from the surface using a lower density wash fluid. 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: Apparatus and methods are disclosed for controlling flow of fluid inside a chamber. A device comprises a chamber comprising at least one wall, a first opening for introducing a fluid into the interior of the chamber, and a second opening opposite the first opening. The at least one wall of the chamber is designed to provide a contracting section, a section having substantially constant cross-sectional area and a diffusing section through the chamber from the first opening to the second opening. The device may be employed as a gas outlet in a reaction chamber for conducting reactions where it is desired to control the internal atmosphere of the reaction chamber. The apparatus may be employed in the manufacture of biopolymers on the surface of a support such as an array of biopolymer features on the support. Also disclosed is a holding element for a support wherein the holding element is a low drag body.