Abstract: A method and apparatus for fabricating replicate arrays of nucleic acid molecules include the preparation of the molecules and the application the molecules onto a substrate in an ordered array. The apparatus comprises a synthesis unit and a plurality of outlets. The synthesis unit comprises a plurality of synthesis chambers that are spatially arranged relative to each other to provide an array suitable for conducting parallel nucleic acid syntheses. The chambers are suitable for containing discrete compositions of nucleic acid molecules. Each outlet of the plurality of outlets communicates with a single synthesis chamber. The plurality of outlets are configured such that nucleic acid molecules can be removed from the chambers through the outlet and deposited onto the substrate in an ordered array that corresponds to the spatial arrangement of the synthesis chambers.

Abstract: The invention concerns a method for detecting impairment of DNA comprising contacting a sample DNA with a composition comprising at least one recognition protein selected from the group consisting of proteins belonging to the nucleotide excision repair system, proteins belonging to the base excision repair system, and proteins belonging to the system for detecting DNA breaks and detecting a complex formed between the recognition protein and DNA to thereby detect impairment of the DNA sequence.

Abstract: Methods are included for quantitating the efficacy of oral care products at dislodging cells from biofilm test surfaces or inhibit or delay the accumulation of cells on a test surface. More specifically, the inventive methods measure the effectiveness of compositions and appliances in a test environment that models biofilm surface orientations that are encountered on a tooth surface, i.e. interproximal and subgingival tooth surfaces. The use of test surfaces that are removably attachable to a tooth prosthesis allow a variety of different quantitative methods to be applied to determine the amount of cells removed or deposited in a biofilm.

Abstract: This invention relates to methods and systems for characterizing the actions of drugs in cells. In particular, the invention provides methods for identifying multiple primary targets through which a drug, drug candidate, or other compound of interest acts on a cell. Thus, the invention also relates to methods for drug development based on the disclosed methods for identifying multiple primary targets of a drug. The methods of the invention involve: (i) measuring responses of cellular constituents to graded exposures of the cell to a drug of interest; (ii) identifying an “inflection concentration” of the drug for each cellular constituent measured; and (iii) identifying “expression sets” of cellular constituents from the distribution of the inflection drug concentrations. Each expression set corresponds to a particular primary target of the drug. The invention also provides computer systems which identify multiple targets of a drug by executing the disclosed methods.

Abstract: This invention provides methods, compositions and apparatus for mapping the regulatory relationship among genes by massive parallel monitoring gene expression. In some embodiments, mutations in the up-stream regulatory genes are detected by monitoring the change in down-stream gene expression. Similarly, the function of a specific mutation in a up-stream gene is determined by monitoring the down-stream gene expression. In addition, regulatory function of a target gene can be determined by monitoring the expression of a large number of down-stream genes. The invention also provides specific embodiments for detecting p53 functional homozygous and heterozygous mutations and for determining the function of p53 mutations.

Abstract: The invention relates to a method for analyzing of determining the methylation pattern of a starting DNA and/or for distinguishing between methylated and non-methylated sites in the starting DNA, comprising at least (A) generating a first DNA fingerprint, containing bands corresponding to both the methylated and non-methylated sites of interest; and/or (B) generating a second DNA fingerprint, containing bands corresponding only to the methylated sites of interest; and optionally comprising (C) generating a third DNA fingerprint, containing bands corresponding only to the non-methylated sites of interest; and optionally further comprising (D) analysing the fingerprint(s) thus obtained. The fingerprints are preferably generated using AFLP, by means of a frequent cutter and a methylation sensitive rare cutter. The invention further relates to specific methods for generating the above first and second DNA fingerprint by means of AFLP, and kits for use with said methods.

Abstract: This invention relates to methods and systems for characterizing the actions of drugs in cells. In particular, the invention provides methods for identifying multiple primary targets through which a drug, drug candidate, or other compound of interest acts on a cell. Thus, the invention also relates to methods for drug development based on the disclosed methods for identifying multiple primary targets of a drug. The methods of the invention involve: (i) measuring responses of cellular constituents to graded exposures of the cell to a drug of interest; (ii) identifying an “inflection concentration” of the drug for each cellular constituent measured; and (iii) identifying “expression sets” of cellular constituents from the distribution of the inflection drug concentrations. Each expression set corresponds to a particular primary target of the drug. The invention also provides computer systems which identify multiple targets of a drug by executing the disclosed methods.

Abstract: The present invention provides for a method for generating a fusion nucleic acid molecule capable of cross-over recombination which comprises: (a) contacting a first pair of primers with a first strand and a second strand of a first nucleic acid molecule and a second pair primers with a first strand and a second strand of a second nucleic acid molecule wherein the primers are suitable for use in a polymerase chain reaction; (b) amplifying the first nucleic acid molecule and the first pair of primers and the second nucleic acid molecule and the second pair of primers under amplification conditions, separately; (c) mixing the amplification products from step (b) and the first primer of the first pair of primers and the second primer of the second pair of primers under hybridization conditions; (d) amplifying the hybridized molecules of step (c) under amplification conditions so as to generate a directed, recombinant fusion nucleic acid molecule capable of cross-over recombination.

Abstract: Described herein are methods and reagents for the selection of protein molecules that make use of RNA-protein fusions.

Abstract: Methods for detecting a nucleotide insertion or deletion in biological samples are described. Methods of the invention are particulary useful for detecting a nucleotide insertion or deletion in regions of polynucleotide repeats. In particular, methods of the invention are useful to detect a nucleotide insertion of deletion at the BAT26 locus.

Abstract: The invention includes kits and methods for assessing the susceptibility of a mammal such as a human for carcinogenesis. The methods comprise determining whether the mammal comprises a certain allele of the mammal's odc gene. The methods include use of a probe which binds specifically with a portion of one allele of the odc gene and which comprises a fluorescent label and a fluorescence quencher. The methods also include use of such a probe and a polymerase enzyme for amplifying a portion of the odc gene, the polymerase having exonuclease activity whereby the probe can be nucleolytically degraded.

Abstract: The malignant or otherwise diseased state of a cell can be determined in tissues fixed by techniques such as the formalin and parafin methods. This determination is made by (1) studying the precise conformation (i.e. position and structure) of at least one gene within a chromosome of a targeted cell and (2) measuring the deviation of gene conformation in comparison to a non-diseased cell. Accordingly, methods for evaluating the malignancy index of cells, as well as monitoring the effectiveness of therapeutic treatment, are provided.

Abstract: The present invention is drawn to a method for identifying Cordyceps sinensis, by amplifying a specimen's 18S rRNA polymorphism by PCR using primer pair NS3 and NS6; digesting the PCR product with restriction enzyme Cfo I; and identifying a genuine Cordyceps sinensis specimen by determining the presence of a PCR product digestible with the restrictions enzyme Cfo I and a DNA fragment in the polymorphism of the specimen belonging to a specific DNA fragment in the polymorphism of Cordyceps sinensis.

Abstract: The present invention relates to spatially-addressable sandwich arrays of compounds, particularly biological compounds such as peptides and polynucleotide probes, and methods of making and using the same. The present invention also relates to a method and device for holding together the substrates of the sandwich array, more particularly, a clamping device for securely yet safely holding substrates of a sandwich array together during assembly, use, storage, and/or transport of the sandwich array.

Abstract: Described herein are methods and reagents for the selection of protein molecules that make use of RNA-protein fusions.

Abstract: The invention relates to the isolation of a nucleic acid molecule which encodes an esophageal cancer associated antigen. Also a part of the invention is the antigen itself, and the uses of the nucleic acid molecule and the antigen.

Abstract: A Nucleic acid ligand “Biochip” is disclosed, consisting of a solid support to which one or more specific Nucleic acid ligands is attached in a spatially defined manner. Each Nucleic acid ligand binds specifically and avidly to a particular Target molecule contained within a Test mixture, such as a Bodily fluid The Target molecules include, but are not limited to, proteins (cellular, viral, bacterial, etc.) hormones, sugars, metabolic byproducts, cofactor, and intermediates, drugs, and toxins. Contacting the Test mixture with the Biochip leads to the binding of a Target molecule to its cognate Nucleic acid ligand. Binding of Target to the Nucleic acid ligand results in a detectable change at each specific location on the Biochip. The detectable change can include, but is not limited to, a change in fluorescence, or a change in a physical parameter, such as electrical conductance or refractive index, at each location on the Biochip.

Abstract: A method is disclosed for detecting the presence of a difference between two related nucleic acid sequences. In the method a complex is formed comprising both strands of each sequence. Each member of at least one pair of non-complementary strands within the complex have labels. The association of the labels as part of the complex is determined as an indication of the presence of a difference between the two related sequences. The complex generally comprises a Holliday junction. In one aspect a medium suspected of containing said two related nucleic acid sequences is treated to provide partial duplexes having non-complementary tailed portions at one end. The double stranded portions of the partial duplexes are identical except for said difference.

Abstract: A genetic analysis device particularly for determining the presence or absence of Single Nucleotide Polymorphisms (SNPs) within specific sequences of DNA. The device includes a housing, at least one glass slide member, and an elastomeric member with channels thereon. Oligo arrays are spotted on the glass slide member(s) and subjected to DNA samples, reagents or the like. A plurality of openings or ports allow entry of samples, reagents or wash materials, while a plurality of exit ports or openings allow removal of such materials. The assay devices can be used for multiple samples or a single sample. A plurality of synthesis devices can be positioned in a support base in order to allow sampling in an automated manner. The synthesis devices can be provided in a 96 well microtiter format.

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.