Abstract: The present invention provides methods of screening for the presence of premalignant melanocytes in a sample from a patient. The methods comprise contacting a nucleic acid sample from a biological sample from the patient with a probe which binds selectively to a target polynucleotide sequence on a chromosomal region which is amplified in melanoma cells.

Abstract: Apparatus for delivering a plurality of different biological materials onto discrete locations on a receiving surface, as for example to fabricate an array of different biological material, includes a plurality of orifices in an orifice member, at least six delivery chambers each in fluid conducting relationship with at least one of the orifices, a plurality of reservoirs each in fluid communication with at least one of the delivery chambers, means associated with each orifice for propelling fluid through the associated orifice from the delivery chamber that is in fluid conducting relationship with the orifice, and a vent for commonly venting at least two of the reservoirs. In some embodiments the chambers and reservoirs are loaded with fluids containing selected biomolecules by drawing the selected fluids into the chambers through the orifices; in other embodiments the fluids are introduced into the reservoirs.

Abstract: Arrays of polynucleotide or polypeptide target molecules immobilized on a surface of a substrate where the target molecules are arranged in the array according to intensity of organism expression of cognate probe molecules which hybridize to the target molecules. For instance, target molecules having a higher than average indicia of hybridization, e.g. at least a factor of 2, are segregated at a peripheral region of the substrate and at a lower surface density. Preferred arrays can contain animal, plant or microorganism target molecules including Aspergillus nidulans. Diagnostic arrays can comprise targets from mixed species, e.g. human, mouse and virus; plant breeding arrays can comprise targets from mixed plants, e.g. Arabidopsis thaliana, maize, soy, cotton, wheat, rice, canola and potato.

Abstract: An instrument for sequencing oligonucleotides is loaded with the products of four sequencing reaction mixtures. These products are a combination of A, C, G and T reaction products for several sequencing reactions. The products of the different sequencing reactions are labeled with fluorescent tags which are distinguishable one from the other on the basis of their excitation or emission spectra. After separation of the oligonucleotides by electrophoresis, the order of the detected peaks is used to call the base sequence.

Abstract: The present invention provides an improved method for stably attaching a desired compound to a silaceous or silane-containing substrate, in particular a glass, porous silica, or oxidized silicon. This method in certain embodiments provides improvements over conventional methods for attaching desired compounds to silaceous or silane-containing substrate, e.g., glass, porous silica, or oxidized silicon materials, e.g. obviating the need for derivatization (e.g., epoxysilane derivatization) prior to attachment. More particularly, the present invention provides a method for stably attaching a desired compound comprising at least one amine and hydroxyl group (e.g., an aminopropanol containing compound), to a silaceous or silane-containing substrate, preferably underivatized (plain) glass, a porous silica, or oxidized silicon substance. The subject method is especially useful for the attachment of nucleic acid sequences, e.g.

Abstract: Triplex complexes contain a single-stranded probe bound to a double-stranded nucleic acid target, in which the probe includes a heteropolymeric nucleic acid or a heteropolymeric nucleic acid analog. All base triplets of the complex are members selected from the group consisting of A-T-A, T-A-T, U-A-T, T-A-U, A-U-A, U-A-U, G-C-G and C-G-C. A cation-facilitated assay includes detecting the presence of such triplex complexes to determine the degree of complementarity between the probe and target sequence. The assay preferably detects a change in fluorescent intensity of a label as a function of binding affinity between the probe and target. The label can be covalently tethered to the probe or to the target, or can be an intercalating fluorophore in the reaction medium.

Abstract: Methods are provide for modifying a solid support, such as a glass slide, by silylating with an agent having the formula H2N—(CH2)n—SiX3 where n is between 1 and 10, and X is independently chosen from OMe, OEt, Cl, Br, or I, then activating with a crosslinking reagent, followed by reacting with an amine-containing polymer. The support can optionally be reacted with a crosslinking reagent again. The support thus modified may be used to make arrays and microarrays where a plurality of targets are stably associated with the support and arranged in a defined manner.

Abstract: The invention provides a homogeneous assay for nucleic acid hybridization. The fluorescent intensity of a hybridization medium containing a probe, a target and an intercalating agent is a function of the hybridization efficiency of the probe with respect to the target. The assay can detect specific hybridization between single-stranded probes and non-denatured double-stranded targets to form triplexes, thus obviating the need to denature the targets. The assay can also detect duplex hybridization complexes. The assay can be used to identify accessible regions in folded nucleotide sequences, to determine the number of mismatched pairs in a hybridization complex, and to map genomes.

Abstract: The present invention provides a method of identifying clones encoding for membranal and secreted proteins by deriving probes from membrane-bound polysomes and free-polysomes, and performing a microarray-based comparison of the relative abundance of the different RNA species. Analysis of the results of such comparison and resultant identification of clones encoding for membranal or secreted proteins, provides an efficient tool for identifying targets of drug development. The present invention further provides a method of augmenting a microarray analysis by utilizing RNA extracted from specific subcellular compartments as templates for DNA probes. The method may be used together with conventional differential analysis techniques for improvement of their analysis and gene identification functions.

Abstract: The present invention concerns an array-based analytical system and method having an enhanced sensitivity which allows for simple and rapid analysis of relative unmodified samples which comprises an analytical system of the type having a plurality of different first members of a specific binding pair affixed in an array thereupon, a mixture including at least one second member of a specific binding pair capable of binding to one of the first members so as to form a specific binding pair which is affixed to the support member, and a reporter system that produces a detectable signal indicative of the presence of the specific binding pair on the support member and wherein the reporter system includes an amplified reporter system that is independent of layering.

Abstract: Different probes each having a specific base sequence are immobilized to each of independent areas formed on the surface of a substrate, complementary polynucleotides in a sample solution are hybridized to the probes, and each of the independent areas on the substrate is heated and then cooled in sequence, and hence the solution is recovered to extract different polynucleotides separately corresponding to individual probes.

Abstract: Methods are provide for modifying a solid support, such as a glass slide, by silylating with an agent having the formula H2N—(CH2)n—SiX3 where n is between 1 and 10, and X is independently chosen from OMe, OEt, Cl, Br, or I, then activating with a crosslinking reagent, followed by reacting with an amine-containing polymer. The support can optionally be reacted with a crosslinking reagent again. The support thus modified may be used to make arrays and microarrays where a plurality of targets are stably associated with the support and arranged in a defined manner.

Abstract: Disclosed is a modular fluorescence sensor having the following general formula: where Fl is a fluorophore, N is a nitrogen atom, Bd1 and Bd2 are independently selected binding groups, Sp is an aliphatic spacer, and An is an anchor group for attaching the sensor to solid substrates. n=1 or 2, m=1 or 2, x is an integer, and y=1 or 2. The binding groups are capable of binding an analyte molecule to form a stable 1:1 complex. In a preferred embodiment, the Bd1 is R1—B(OH)2 and Bd2 is R2—B(OH)2. R1 and R2 are aliphatic or aromatic functional groups selected independently from each other and B is a boron atom. The present invention also provides methods of synthesizing a modular fluorescence sensor and its use in labeling solid substrates.

Abstract: Probes comprise S1 and P1 nuclease (as an enzyme label) linked to a specific binding member such as a nucleotide sequence or an antibody. Such probes are useful for sandwich assays. As compared with known probes using alkaline phosphatase as a label, advantages include relative insensitivity to phosphate and elevated temperature and reduced risk of nonspecific binding.

Abstract: Different probes each having a specific base sequence are immobilized to each of independent areas formed on the surface of a substrate, complementary polynucleotides in a sample solution are hybridized to the probes, and each of the independent areas on the substrate is heated and then cooled in sequence, and hence the solution is recovered to extract different polynucleotides separately corresponding to individual probes.

Abstract: Solid substrates and methods for their preparation are provided, where enhanced functionalization of solid substrates is achieved, so that higher levels of binding of a wide variety of moieties can be obtained. The surface is nitrated with a nitronium agent, where the nitro groups may be modified in a variety of ways to serve as sites for linking. The resulting solid substrates find use in therapy, diagnosis and processing.

Abstract: Method of making an electrotransport device containing an analog of a parent polypeptide having one or more amino acid residues substituted relative to the parent polypeptide with an amino acid residue selected from the group consisting of proline, glycine and asparagine.

Abstract: Methods and model systems for identifying and characterizing new therapeutic agents, particularly proteins, which mimic or inhibit the activity of all interferons, Type I interferons, IFN-&agr;, IFN-&bgr;, or IFN-&ggr;. The method comprises administering an interferon selected from the group consisting of IFN-&agr;, IFN &bgr;, IFN-&tgr;, IFN-&ohgr;, IFN-&ggr;, and combinations thereof to cultured cells, administering the candidate agent to a duplicate culture of cells; and measuring the effect of the candidate agent and the interferon on the transcription or translation of one or, preferably, a plurality of the interferon stimulated genes or the interferon repressed genes (hereinafter referred to as “ISG's” and “IRGs”, respectively). The model system is an array with gene probes that hybridize with from about 100 to about 5000 ISG and IRG transcripts.

Abstract: Array hybridization can be facilitated by agitating a reaction cell subject to centrifugal force greater than 1G. A two-dimensional hybridization array is preferably oriented generally orthogonal to the centrifugal force. Agitation involves titling the array back and forth about an axis, preferably parallel to a centrifuge axis. The centrifugal force serves, in a sense, as supergravity helping to overcome non-specific binding forces (viscous forces and other forces at the liquid-solid boundary) that limit the rate of liquid flow. Thus, the agitation rate and the related replenishment rate can be increased. The agitation causes the sample liquid to wash back and forth across the array, which remains protected by a thin liquid film. The resulting “tidal” motion, results in thorough mixing of the sample liquid. In addition, since only a thin film is required over much of the array, typically costly sample volume can be reduced. Thus, faster hybridization with lower sample volumes can be achieved.

Abstract: A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.