Abstract: Methods for correlating genes and gene function are provided. Such methods generally involve selecting a candidate gene that appears to be correlated with a particular cellular state or activity and then validating the role of the candidate gene in establishment of such a cellular state or activity. Certain methods utilized RNA interference techniques in the validation process.

Abstract: The present disclosure describes the use of genetic variance information for folate transport or metabolism genes or pyrimidine transport or metabolism genes in the selection of effective methods of treatment of a disease or condition. The variance information is indicative of the expected response of a patient to a method of treatment. Methods of determining relevant variance information and additional methods of using such variance information are also described.

Abstract: The invention provides novel extracts, proteins, and complexes that improve the polymerization activity of nucleic acid polymerases. Included within the aspects of the invention are methods for identifying compositions with a polymerase enhancing activity, methods for purifying and using these compositions, and specific extracts, proteins, and complexes that function to enhance polymerase activity. As an example, specifically described is nucleotide and amino acid sequence information for a Pyrococcus furiousus PEF (P45), which was used to produce a recombinant PEF.

Abstract: A set of a plurality of microsatellite markers is provided for plant species of the tribe Triticeae, particularly Triticum aestivum. Each of the markers are constituted by a sequence tagged site (STS) defined by two primers, specific to a particular microsatellite sequence. Each primer has an average length of 20±3 bases and flanks the particular microsatellite sequence. Each of the microsatellite markers is formed by amplification of the microsatellite sequence by a polymerase chain reaction, to form markers of different length.

Abstract: A method detects binding of molecules, advantageously without tagging molecules in the sample. A sensor is used in which is included a single stranded nucleic acid sequence and a photoluminescent material in respective layers. After the sensor is exposed to a biological sample for sufficient time for its single stranded nucleic acid sequence to bind to a material of interest, photoluminescence from the sensor can be measured. An apparatus for tagging-free detection of binding of molecules also is provided. Methods of making tagging-free sensors are provided. Also, tagging-free methods to detect binding of antigens and related devices are disclosed.

Abstract: A genome DNA analysis method and a genome DNA analysis system of the present invention generates multiply-charged ions with 5 or more electric charges by an ionization process using air atomization. Also, a mass spectrometric spectrum thereof is detected and compared with predicted mass spectrum patterns in the presence or absence of polymorphism to determine a base at a polymorphic point.

Abstract: Disclosed are methods and reagents for detecting nucleotide mismatches (for example, due to sequence variances) in a nucleic acid sample involving the use of a nucleic acid probe derived from a hemizygous cell. Methods for determining the haplotype of a nucleic acid sample are also disclosed. Also disclosed are methods for producing the probe and kits containing the probe.

Abstract: A carrier for gene detection as a means for prediction before treatment whether interferon therapy is valid or not for a patient, a method for detection of interferon therapy for an individual, an apparatus for gene detection, and a kit for detection of validity of interferon therapy.

Abstract: Methods and kits that use nucleotide analogs to confer increased accuracy and improved resolution in the analysis and sequencing of oligonucleotide mixtures are provided.

Abstract: Processes are disclosed using the depolymerization of a nucleic acid hybrid to qualitatively and quantitatively analyze for the presence of predetermined nucleic acid target sequences using a multiplex assay format. Applications of those processes include the detection of single nucleotide polymorphisms, identification of single base changes, speciation, genotyping, medical marker diagnostics, and the like.

Abstract: The present invention relates to a herbal chip comprising a plastic slide, a coating as a spacer on the plastic slide, and fractions or components obtained from herbs that are independently allocated in microarrays on the coating. The herbal chip is useful for screening for active ingredients contained in the herbs that have specific pharmacological or therapeutical functions.

Abstract: A method is provided for producing a library of mutagenized polynucleotides from a target sequence comprising (a) taking a sample comprising: (i) a target sequence including a section to be mutagenized, (ii) a library of first primers where the first primers include a first fixed sequence and a first unknown sequence 3′ to the first fixed sequence, the first unknown sequence varying within the library of first primers, and (iii) a library of second primers where the second primer include a second fixed sequence that differs from the first fixed sequence, and a second unknown sequence 3′ to the second fixed sequence, the second unknown sequence varying within the library of second primers; (b) performing one or more cycles of primer extension amplification on the sample in the presence of at least one polymerase such that a member of the library of the first primers is extended relative to the target sequence; and (c) performing one or more additional cycles of primer extension amplification on the

Abstract: Allelic variation in the vex2, pep27 and vncS genes of bacteria responsible for tolerance to antibiotics such as penicillin and vancomycin, is taught. Methods for identifying antibiotic tolerant bacteria and subjects infected with such bacteria, particularly antibiotic tolerant Streptococcus pneumoniae, are provided. Test kits and components useful for performing such methods, particularly including oligonucleotide primers, are also provided.

Abstract: The present invention provides methods for screening compounds capable of modulating nucleic acid-modifying enzymatic activity, including topoisomerase activity.

Abstract: The determination of base (nucleotide) composition in DNA by mass spectrometry is described. Accurate and efficient analyses of the enormous pool of DNA sequences are required for; (a) validation of DNA sequences; (b) comparison of a parent (known) sequence with a related (unknown) sequence, and (c) characterization of sequence polymorphisms in various genes especially those associated with genetically inherited human diseases. The combination of stable isotope-labeling of PCR products of target sequences with analysis of the mass shifts by mass spectrometry (MS) is shown to provide such analyses, since the mass-shift due to the labeling of a single type of nucleotide (i.e., A, T, G, or C) identifies the number of that type of nucleotide in a given DNA fragment. Accurate determinations of nucleotide compositions of DNA fragments have been achieved with an accuracy of ±0.03% with respect to their known sequences. The method has also been applied to identify a known single-nucleotide polymorphism (SNP).

Abstract: The present invention features inhibitors of target-independent amplification and the use of such inhibitors for enhancing an amplification protocol. The inhibitors are believed to enhance an amplification protocol by inhibiting the ability of one or more nucleic acid polymerases to use nucleic acid in a polymerase reaction in the absence of target nucleic acid.

Abstract: A method for synthesizing a nucleic acid molecule comprising at least one non-canonical nucleoside triphosphate using a mutant polymerase having a reduced discrimination between canonical and non-canonical substrates is disclosed. The method comprises incubating a template nucleic acid in a reaction mixture comprising the mutant nucleic acid polymerase and the appropriate canonical and non-canonical nucleoside triphosphates which are desired substrates for the mutant nucleic acid polymerase. The present invention is also a method of determining the sequence of a nucleic acid molecule using the mutant polymerase to create a nucleic acid molecule comprising at least one non-canonical nucleoside triphosphate.

Abstract: The present invention relates to a method for detecting the amount of a target polynucleotide in a sample. A combination is provided in a medium. The combination comprises (i) a sample suspected of containing the target polynucleotide, the target polynucleotide being in single stranded form, (ii) a reference polynucleotide comprising a sequence that is common with a sequence of the target polynucleotide, and (iii) a predetermined amount of an oligonucleotide probe that has a sequence that hybridizes with the sequence that is common. The combination is subjected to conditions for amplifying the target polynucleotide and the reference polynucleotide. The conditions permit formation of substantially non-dissociative complexes of the target polynucleotide and the reference polynucleotide, respectively, with the oligonucleotide probe. Furthermore, the predetermined amount of the oligonucleotide probe is less than the expected amount of the amplified target polynucleotide.

Abstract: The invention is based on the reaction of recombinagenic oligonucleotides in a cell-free system containing a cytoplasmic cell extract and a test duplex DNA on a plasmid. The reaction specifically converts a mutant kanr gene to recover the resistant phenotype in transformed MutS, RecA deficient bacteria and allows for the rapid and quantitative comparison of recombinagenic oligonucleobases. Using this system a type of Duplex Mutational Vector termed a Heteroduplex Mutational Vector, was shown to be more active in than the types of mutational vectors heretofore tested. Further improvements in activity were obtained by replacement of a tetrathymidine linker by a nuclease resistant oligonucleotide, such as tetra-2′-O-methyl-uridine, to link the two strands of the Duplex Mutational Vector and removal of the DNA-containing intervening segment. The claims concern Duplex Mutational Vectors that contain the above improvements.

Abstract: Yeast strains carrying a human wild-type TP53 are employed to select for mutations. The types of mutations can be analyzed genetically as recessive or dominant-negative. The mutational spectrum of dominant-negative TP53 mutants selected in yeast correlates tightly with TP53 mutations found in human cancers. Thus the use of such yeast assays is validated for studying the effects of various agents on human TP53, one of the most important and ubiquitous of human cancer genes. Assays, kits, and constructs are provide which use yeast as a genetic system for making and studying human TP53 mutations. Such assays can be used to develop therapeutic agents, to study putative carcinogens, and to identify other cellular components which interact with p53 and abrogate its activity.