Abstract: The invention concerns a method for the identification of cytosine methylation patterns in genomic DNA samples, wherein a) a genomic DNA sample is chemically treated such that cytosine and 5-methylcytosine react differently and a different base pairing behavior of the two products results in the duplex; b) parts of the thus-treated DNA sample are enzymatically amplified; c) the amplified parts of the thus-treated DNA sample bind to a surface; d) a set of probes of different nucleobase sequences, each of which contains the dinucleotide sequence 5?-CpG-3? at least once, is hybridized to the immobilized DNA sample; e) the non-hybridized probes are separated; f) the hybridized probes are analyzed in a mass spectrometer, wherein the position of the probes on the sample holder permits a classification of the hybridizing DNA sample; g) Assignment of the peak pattern obtained from the mass spectra to the methylation pattern and comparison of the new data with a database.

Abstract: Disclosed is substantially pure DNA encoding mammalian IAP polypeptides; substantially pure polypeptides; and methods of using such DNA to express the IAP polypeptides in cells and animals to inhibit apoptosis. Also disclosed are conserved regions characteristic of the IAP family and primers and probes for the identification and isolation of additional IAP genes. In addition, methods for treating diseases and disorders involving apoptosis are provided.

Abstract: Methods for discriminating between fully complementary hybrids and those that differ by one or more base pairs and libraries of unimolecular, double-stranded oligonucleotides on a solid support. In one embodiment, the present invention provides methods of using nuclease treatment to improve the quality of hybridization signals on high density oligonucleotide arrays. In another embodiment, the present invention provides methods of using ligation reactions to improve the quality of hybridization signals on high density oligonucleotide arrays. In yet another embodiment, the present invention provides libraries of unimolecular or intermolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA.

Abstract: The methods and apparatus disclosed herein concern nucleic acid sequencing by enhanced Raman spectroscopy. In certain embodiments of the invention, nucleotides are covalently attached to Raman labels before incorporation into a nucleic acid 13. Exonuclease 15 treatment of the labeled nucleic acid 13 results in the release of labeled nucleotides 16, 130, which are detected by Raman spectroscopy. In alternative embodiments of the invention, nucleotides 16, 130 released from a nucleic acid 13 by exonuclease 15 treatment are covalently cross-linked to silver or gold nanoparticles 140 and detected by surface enhanced Raman spectroscopy (SERS), surface enhanced resonance Raman spectroscopy (SERRS) and/or coherent anti-Stokes Raman spectroscopy (CARS). Other embodiments of the invention concern apparatus 10, 100, 210 for nucleic acid sequencing.

Abstract: The present invention provides for the identification and cloning of functional plant centromeres in Arabidopsis. This will permit construction of stably inherited minichromosomes which can serve as vectors for the construction of transgenic plant and animal cells. In addition, information on the structure and function of these regions will prove valuable in isolating additional centromeric and centromere related genetic elements and polypeptides from other species.

Abstract: A method of genotyping single nucleotide polymorphisms (“SNP”) and point mutations in nucleic acid based on chain extension by polymerase. This invention is based on the fact that the nucleoside immediately 5? adjacent to any SNP/point mutation site is known, and the neighboring sequence immediately 3? adjacent to the site is also known. A primer complementary to the sequence directly adjacent to the SNP on the 3? side in a target polynucleotide is used for chain elongation. The polymerase reaction mixture contains one chain-terminating nucleotide having a base complementary to the nucleotide directly adjacent to the SNP on the 5? side in the target polynucleotide. An additional dNTP may be added to produce a primer with the maximum of a two-base extension. The resultant elongation/termination reaction products are analyzed for the length of chain extension of the primer, or for the amount of label incorporation from a labeled form of the terminator nucleotide.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Abstract: The present invention describes a method for separating or partially separating heteroduplex and homoduplex DNA molecules in a mixture. In the method, the mixture is applied to an anion-exchange chromatography medium. The heteroduplex and homoduplex molecules are eluted with a mobile phase containing an eluting salt, including an anion and a cation, a buffer, and preferably including an organic solvent. The eluting is carried out under conditions effective to at least partially denature the heteroduplexes (e.g., thermal or chemical denaturing) resulting in the separation of the heteroduplexes from the homoduplexes. The method has many applications including, but not limited to, detecting mutations and comparative DNA sequencing.

Abstract: The invention features a method for multiplexed analysis of a plurality of target nucleic acid sequences in a sample. The method provides a derivative nucleic acid for each target sequence analyzed and present in the sample.

Abstract: The invention relates to improved methods of detecting and characterizing polynucleotide sequences and variations in polynucleotide sequences. The invention further relates to a device that can be used to detect and characterize polynucleotide sequences and variations in polynucleotide sequences.

Abstract: This invention relates to methods, kits and compositions suitable for the improved detection, analysis and quantitation of nucleic acid target sequences using probe based hybridization assays. The invention is more specifically directed to methods, kits and compositions suitable for suppressing the binding of detectable nucleic acid probes or detectable PNA probes to non-target nucleic acid sequences in an assay for a target nucleic acid sequence to thereby improve the reliability, sensitivity and specificity of the assay. The methods, kits and compositions of this invention are particularly well suited to the detection and analysis of nucleic acid point mutations.

Abstract: A method in which a temperature gradient is generated across a “gradient” block, and an apparatus comprising a block across which a temperature gradient can be generated. By setting up such a gradient, multiple reaction mixtures held in wells on the gradient block can be simultaneously run at temperatures which differ only slightly, thereby permitting an optimum temperature for the reaction to be quickly identified. In a preferred embodiment the gradient block is integrated into a thermal cycler used for nucleic acid amplification reactions.

Abstract: Novel oligomers are disclosed which have enhanced ability with respect to forming duplexes or triplexes compared with oligomers containing only conventional bases. The oligomers contain the bases 5-(1-propynyl)uracil, 5-(1-propynyl)cytosine or related analogs. The oligomers of the invention are capable of (i) forming triplexes with various target sequences such as virus or oncogene sequences by coupling into the major groove of a target DNA duplex at physiological pH or (ii) forming duplexes by binding to single-stranded DNA or to RNA encoded by target genes. The oligomers of the invention can be incorporated into pharmaceutically acceptable carriers and can be constructed to have any desired sequence, provided the sequence normally includes one or more bases that is replaced with the analogs of the invention.

Abstract: The present invention provides materials and methods for preventing stenosis or restenosis of a blood vessel using Vascular Endothelial Growth Factor C (VEGF-C) and/or Vascular Endothelial Growth Factor D (VEGF-D) genes or proteins.

Abstract: The invention provides a method for generating a polynucleotide sequence or population of sequences from parent single stranded polynucleotide sequences encoding one or more protein motifs, comprising the steps of (a) providing single stranded DNA constituting plus and minus strands of parent polynucleotide sequences; (b) digesting the single stranded polynucleotide sequences with a nuclease other than DNase I to generate populations of single stranded fragments; (c) contacting said fragments generated from the plus strands with fragments generated from the minus strands and optionally, adding primer sequences that anneal to the 3? and 5? ends of at least one of the parent polynucleotides under annealing conditions; (d) amplifying the fragments that anneal to each other to generate at least one polynucleotide sequence encoding one or more protein motifs having altered characteristics as compared to the one or more protein motifs encoded by said parent polynucleotides.

Abstract: A method of inhibiting the self-splicing of a Group I intron is disclosed. The method uses an oligonucleotide having a sequence essentially identical to a guide sequence found in the 5? flanking exon and terminates with a 3? ribonucleoside. Usually the oligonucleotide has N3??P5? phosphoramidate or N3??P5? thiophiosphoramidate linkages rather than phosphodiester linkages. A method of inhibiting the growth of organisms having Group I intron, particularly certain pathogenic fungi including P. carinii, C. albicans, and A. nidulans using the oglionucleotide is also provided.

Abstract: The invention provides a method that allows the construction of a chimeric and/or modified and/or reconstructed DNA molecule from two DNA fragments in a defined order and orientation, and to clone the molecule one step in a suitable vector using site specific recombination. No initial step of classical cloning via restriction enzymes is needed, in contrast to the classical recombination systems. This method allows the reliability of the recombination method for cloning with the flexibility of PCR to introduce modifications in the insert sequence. Moreover, this method allows the construction of chimerical DNA molecules associating two different elements, such as promoter-gene association or fusion proteins.

Abstract: The invention provides a new primer composition for detecting the presence of Shigella sonnei and a method of using the same. The primer composition and method have high specificity and sensitivity on the detection of Shigella sonnei.

Abstract: The present invention relates to prognostic methods which are useful in medicine, particularly cancer chemotherapy. The object of the invention to provide a method for assessing Dihydropyrimidine dehydrogenase (DPD) expression levels in tissues and prognosticate the probable resistance of a patient's tumor to treatment with 5-FU based therapies by examination of the amount of DPD mRNA in a patient's tumor cells and comparing it to a predetermined threshold expression level. More specifically, the invention provides to oligonucleotide primer pairs DPD3A and DPD3B and methods comprising their use for detecting levels of Dihydropyrimidine dehydrogenase (DPD) mRNA.

Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.