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: A method and apparatus for fabricating an array of polynucleotides on a substrate. A polynucleotide deposition system is operated to deposit an array of polynucleotide containing fluid droplets on the substrate and which, when dry, will yield polynucleotide containing spots of respective target locations and dimensions. Droplets deposited by the system are allowed to dry to yield actual spots. An image is captured of the substrate with dried actual spots. Dried actual spot locations or dimensions from the image, are compared with target locations or dimensions of polynucleotide containing spots. A signal indicative of the result of the comparison may be generated.

Abstract: A method and apparatus for fabricating an array of polynucleotides on a substrate. A polynucleotide deposition system is operated to deposit an array of polynucleotide containing fluid droplets on the substrate and which, when dry, will yield polynucleotide containing spots of respective target locations and dimensions. Droplets deposited by the system are allowed to dry to yield actual spots. An image is captured of the substrate with dried actual spots. Dried actual spot locations or dimensions from the image, are compared with target locations or dimensions of polynucleotide containing spots. A signal indicative of the result of the comparison may be generated.

Abstract: A method and apparatus for fabricating an array of polynucleotides on a substrate. A polynucleotide deposition system is operated to deposit an array of polynucleotide containing fluid droplets on the substrate and which, when dry, will yield polynucleotide containing spots of respective target locations and dimensions. Droplets deposited by the system are allowed to dry to yield actual spots. An image is captured of the substrate with dried actual spots. Dried actual spot locations or dimensions from the image, are compared with target locations or dimensions of polynucleotide containing spots. A signal indicative of the result of the comparison may be generated.

Abstract: Methods of identifying a sequence of a probe, e.g., a biopolymeric probe, such as a nucleic acid, that is suitable for use as a surface immobilized probe for a target molecule of interest, e.g., a target nucleic acid, are provided. A feature of the subject methods is that a set of computationally determined initial candidate sequences are empirically evaluated to obtain functional data that is then employed to identify one or more clusters of candidate probe sequences from the initial set such that all candidate probe sequences within each identified cluster exhibitsubstantially the same performance under a plurality of different experiments, specifically a plurality of differential gene expression experiments. A candidate probe from the cluster that exhibits the best performance across the plurality of experimental sets is then selected as the optimum candidate probe, e.g., based on one or more performance metrics.

Abstract: Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e.g., by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

Abstract: A method, apparatus and computer program product, for fabricating an array of biopolymers on a substrate. The method uses a biopolymer or biomonomer fluid and a drop dispenser having a chamber into which the fluid is loaded and an orifice communicating with the chamber from which the fluid is dispensed. The method includes, when the chamber is loaded, applying a prime pressure to the fluid which varies over a range sufficient to move fluid within the drop dispenser but insufficient to cause fluid to be dispensed from the orifice. Drops are dispensed from the dispenser to the substrate so as to form the array.

Abstract: A method of fabricating an addressable array of biopolymer probes on a substrate according to a target array pattern using a deposition apparatus, and a deposition apparatus which can execute the method and computer program products for the apparatus. The deposition apparatus which, when operated according to a target drive pattern based on nominal operating parameters of the apparatus, provides the probes on the substrate in the target array pattern. The method includes examining at least one operating parameter for an error from a nominal value which error will result in use of the target drive pattern producing a discrepancy between the target array pattern and an actual array pattern deposited. When an error is detected deriving, based on the error, a corrected drive pattern different from the target drive pattern such that use of the corrected drive pattern results in a reduced discrepancy between the target and actual array patterns.

Abstract: An apparatus and method are provided for producing and inspecting a plurality of deposited features in a pattern on a portion of a substrate surface, as in an oligonucleotide array. The apparatus comprises a printhead for depositing a fluid to form the array of features on the substrate surface and a camera for imaging the deposited features. The apparatus also comprises a printhead controller for positioning and activating the inkjet printhead to deposit the array features. The camera, e.g., a digital line scan camera, is controlled by a camera controller such that the camera acquires images corresponding to substantially only the portion of the surface on which features should have been deposited. The camera and printhead are preferably situated such that an induced movement of the printhead relative to the substrate results in a substantially identical corresponding movement of the camera.

Abstract: A method of fabricating an array with multiple sets of neighboring features. In the method, for each of multiple sets of neighboring features, at least one set of drops is deposited from a corresponding same pulse jet dispenser onto a substrate so as to form the array with the sets formed from drops deposited by respective different dispensers. Apparatus and computer program products which can execute a method of the invention, are also provided.

Abstract: A method of fabricating an array of different chemical moieties. The method may include ejecting drops containing the different moieties or precursors thereof from an orifice in an ejector head onto a substrate surface spaced from the orifice so as to form the array. The substrate surface may have structures adjacent each of multiple feature locations so as to assist in confining drops ejected onto the surface to the feature locations, which structures comprise channels or deposited raised members adhering to the surface and extending above adjacent feature locations. An array of different chemical moieties is also provided which has features at respective locations on a planar substrate surface having structures comprising channels or deposited raised barriers adhering to the surface, and which structures are adjacent each of multiple feature locations.

Abstract: A method, apparatus and computer program product, for fabricating an array of biopolymers on a substrate. The method uses a biopolymer or biomonomer fluid and a drop dispenser having a chamber into which the fluid is loaded and an orifice communicating with the chamber from which the fluid is dispensed. The method includes, when the chamber is loaded, applying a prime pressure to the fluid which varies over a range sufficient to move fluid within the drop dispenser but insufficient to cause fluid to be dispensed from the orifice. Drops are dispensed from the dispenser to the substrate so as to form the array.

Abstract: A method, apparatus, and computer program, for fabricating multiple arrays arranged successively in a first direction on a substrate and each having multiple feature sets arranged successively in the first direction within the array. The method uses a head system having multiple successive sets of dispensers. In the method, the head system is advanced in the first direction over the substrate while dispensing drop sets for each array from dispenser sets so as to form the arrays. In one aspect, drop sets are dispensed in an order the reverse of that from which the dispenser sets pass over a given location on the substrate as the head system advances in the first direction. In this case, each dispenser set deposits a drop set at a distance ahead of a drop set deposited by a preceding dispenser set which is less than the distance to the successive drop dispenser set which deposits the next drop set.

Abstract: A method, apparatus, and computer program products for fabricating multiple chemical arrays on a substrate, each array having multiple rows of feature locations with arrays of different sets being arranged in a sideways orientation with respect to the rows. The method includes dispensing drops from a drop dispensing head onto the substrate while maintaining a gap between the head and substrate and moving them relative to one another along a path so as to fabricate the arrays. The path for the relative moving includes moving the head in a direction along the rows of a first array set then moving the head in an opposite direction along the rows of a second array set. This pattern is repeated with the second array set of an earlier cycle being the first array set of a later cycle.

Abstract: A method, apparatus, and computer program products useful in fabricating a chemical array. The apparatus may include a head system, transport system, and a processor. The head system has multiple groups of drop dispensers. The transport system moves the head system with respect to a substrate. The processor dispenses drops from dispensers during operation of the transport system, in a pattern along a selected path for each group. The method, apparatus, and computer program products provide a means by which error dispensers can readily be replaced by redundant non-error dispensers loaded with the same fluid.

Abstract: A method of fabricating an array with multiple sets of neighboring features. In the method, for each of multiple sets of neighboring features, at least one set of drops is deposited from a corresponding same pulse jet dispenser onto a substrate so as to form the array with the sets formed from drops deposited by respective different dispensers. Apparatus and computer program products which can execute a method of the invention, are also provided.

Abstract: Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.

Abstract: A method of generating an addressable array of biopolymers on a substrate. The biopolymers may be obtained from individual identified vessels. The obtained biopolymers are deposited onto different regions of the substrate so as to fabricate the array. A map of the identity of the vessels to the corresponding regions of the substrate onto which the biopolymers from respective vessels are deposited, is saved in a memory in association with a map identifier. The map identifier is applied to the substrate or a housing carrying the substrate. The fabricated array with applied map identifier is shipped to a remote location. A method of using such an array, apparatus, and computer programs for executing the methods, are also provided.

Abstract: Methods and reagents are disclosed which provide for more sensitive, more accurate and higher through-put analyses of target nucleic acid sequences. The methods and reagents of the present invention may be generically applied to generally any target nucleic acid sequence and do not require a priori information about the presence, location or identity of mutations in the target nucleic acid sequence. The reagents of the invention are mixtures of oligonucleotide precursors having a high level of coverage and mass number complexity, and also having tags analyzable by mass spectrometry which are covalently linked to the precursors through cleavable bonds. A method is also disclosed for analyzing a target nucleic acid sequence employing the mixtures of oligonucleotide precursors having tags analyzable by mass spectrometry covalently linked to the oligonucleotide precursors through cleavable bonds, and chemical or enzymatic assays to alter the mass of the oligonucleotide precursors prior to mass spectral analysis.

Abstract: A method and apparatus for fabricating an array of biopolymers on a substrate using a biopolymer or biomonomer fluid, and using a dispensing head. The head has a reservoir chamber and at least one jet which can dispense droplets onto a substrate. The jet includes a capillary delivery chamber communicating with the reservoir chamber, which delivery chamber has an orifice. The jet further includes an ejector which, when activated, causes a droplet to be ejected from the orifice. The method includes loading the head by positioning the head with the orifice adjacent and facing a biomonomer or biopolymer fluid, and providing a load pressure to the reservoir chamber. The load pressure is sufficiently negative such that the fluid is drawn into the reservoir chamber through the orifice and delivery chamber, while simultaneously being insufficient to result in ambient atmosphere entering the delivery chamber through the orifice once the head has been loaded and no further fluid is facing and adjacent the orifice.