| Element-tagged olignucleotide gene expression analysis -> Monitor Keywords |
|
|
 
Element-tagged olignucleotide gene expression analysisElement-tagged olignucleotide gene expression analysis description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20070190560, Element-tagged olignucleotide gene expression analysis. Brief Patent Description - Full Patent Description - Patent Application Claims
CROSS-REFERENCE TO RELATED APPLICATIONS [0001]This application claims priority to U.S. Provisional Patent Application 60/772,588 filed Feb. 13, 2006 entitled "Metal-tagged oligonucleotide gene expression analysis by ICP-MS", the entire contents of which are herein incorporated by reference. COPYRIGHT AND LEGAL NOTICES [0002]A portion of the disclosure of this patent document contains material which is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent files or records, but otherwise reserves all copyrights whatsoever. FIELD [0003]The invention relates to a rapid and sensitive assay employing elemental analysis for gene expression analysis using complementary oligonucleotides labeled with element tags or attached to element imbibed supports. INTRODUCTION [0004]Biological "samples" refers to any sample of a biological nature that requires analysis. For example, samples may include biological molecules, tissue, fluid, and cells of an animal, plant, fungus, or bacteria. They may also include molecules of viral origin. Typical samples include, but are not limited to, sputum, blood, blood cells (e.g., white cells), tissue or fine needle biopsy samples, urine, peritoneal fluid, and pleural fluid, or cells there from. Biological samples may also include sections of tissues such as frozen sections taken for histological purposes. Another typical source of biological samples are viruses and cell cultures of animal, plant, bacteria, fungi where gene expression states can be manipulated to explore the relationship among genes. Other examples are known to those skilled in the art. [0005]RNA sample" is an ribonucleic acid (RNA) preparation of a biological sample. It includes not only the mature mRNA, but also the RNA processing intermediates and nascent pre-mRNA transcripts. For example, total mRNA purified with poly (T) column contains RNA molecules with poly (A) tails. Those poly A+ RNA molecules could be mature mRNA, RNA processing intermediates, nascent transcripts or degradation intermediates. [0006]Nucleic acid" as used herein refers to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form such as any DNA or RNA or DNA/RNA hybrid molecule. The term refers to any DNA including, but not limited to, genomic DNA, mitochondrial DNA, plasmid DNA, chloroplast DNA, cDNA, amplified DNA or RNA fragments, total RNA, messenger RNA, small nuclear RNA. [0007]Oligonucleotide" is a single-stranded nucleic acid ranging in length from 2 to about 1000 nucleotides, more typically from 2 to about 500 nucleotides in length. It may also include "locked nucleic acid" molecules (LNA). [0008]LNA" refers to bi-cyclic high-affinity RNA analogs in which the furanose ring of the ribose sugar is chemically locked in an RNA-mimicking conformation by the introduction of an O2',C4'-methylene bridge, resulting in unprecedented hybridization affinity toward complementary DNA and RNA molecules. The thermal stability and improved mismatch discrimination of short LNA-modified oligonucleotides has made them useful for single nucleotide polymorphism (SNP) genotyping assays, antisense-based gene silencing and gene expression profiling. [0009]Target nucleic acid" refers to a nucleic acid (often derived from a biological sample and hence referred to also as a sample nucleic acid), to which a complementary oligonucleotide probe specifically hybridizes. The target nucleic acids can be derived from any source of nucleic acids (e.g., including, but not limited to chemical syntheses, amplification reactions, forensic samples, etc.). It is either the presence or absence of one or more target nucleic acids that are to be detected, or the amount of one or more target nucleic acids that is to be quantified. The target nucleic acid(s) that are detected preferentially have nucleotide sequences that are complementary to the nucleic acid sequences of the corresponding oligonucleotide probe(s) to which they specifically bind (hybridize). The term target nucleic acid may refer to the specific subsequence of a larger nucleic acid to which the probe specifically hybridizes, or to the overall sequence (e.g., gene or mRNA) whose abundance (concentration) and/or expression level it is desired to detect. Other variations of this definition are known to those skilled in the art. [0010]Probe" refers to a nucleic acid that binds to a target nucleic acid of complementary sequence through complementary base pairing, usually hydrogen bond formation. As used herein, an oligonucleotide probe may include natural (i.e. A, G, C, or T) or modified bases (for example, but not limited to, 7-deazaguanosine, inosine, etc.) as is known to those skilled in the art. In addition, the bases in an oligonucleotide probe may be joined by a linkage other than a phosphodiester bond, so long as it does not interfere with hybridization. Thus, oligonucleotide probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages. Expression of a particular transcript may be detected by a plurality of probes, typically, 5, 10, 15, 20, 30 or 40 probes. Each of the probes may target different sub-regions of the transcript. However, probes may overlap over targeted regions. Probes may be selected or designed using a selection program such as Primer3 from Massachusetts Institute of Technology (MIT). According to the invention, probes may be labeled with an elemental tag at the 3' or 5' end, or in the middle of the oligonucleotide. In one embodiment, the probes are immobilized to the support through the one of the ends. Other examples of probe are known to those skilled in the art. [0011]A support" is a surface which has been functionalized by, for example, pyrrole-2,5-dione(maleimido), sulfonic acid anion, or p-(chloromethyl)styrene but not limited to these. A support may, for example, be a synthetic membrane, bead (polystyrene, agarose, silica, etc), planar surface in plastic microwells, glass slides, reaction tubes, etc (not limited to these). The function of a support is to act as a solid phase for the coupling of probes or target molecules. Yet in another variation of this definition, which is known to those skilled in the art, the support means any surface between two different states of matter: liquid and solid, solid and solid, liquid and liquid, liquid and gas, gas and solid and so on. [0012]Coupled to a support" means bound directly or indirectly thereto including attachment by covalent binding, hydrogen bonding, ionic interaction, hydrophobic interaction, or using specific ligands attached to the end of the oligonucleotide probe for specific interaction with ligand-binding molecules attached to the support, for example a bead. For example, such a system may include biotin-streptavidin, where the probe carries a biotin moiety and the support is coated with streptavidin. Covalent chemical attachment of the oligonucleotide probe to the support can be accomplished through the 5'-phosphate on the nucleic acid to the coated support through a phosphamidate bond. Coupled to support may be achieved by means of a spacer molecule to provide a space between the double stranded part of the probe and target1. Such methods for the immobilization of oligonucleotides to supports are well established in the art.sup.2-4. Yet in another variation of this definition, which is known to those skilled in the art, the coupling to support means functional attachment to boundary between two different states of matter: liquid and solid, solid and solid, liquid and liquid, liquid and gas, gas and solid and so on. [0013]Element labeled bead" is a type of support bead (for example, but not limited to, polystyrene, agarose, silica, etc) which functionally incorporates or is imbibed with an element or multitude of elements with one or many isotopes. As is known to those skilled in the relevant arts, an element can be an atomic part of chemical moiety. [0014]Uniquely labeled bead" refers to a physical entity of a multitude of atoms of one or more isotopes of one or more elements imbibed in a bead such that one type of said bead labeled with one type of said elements is distinguishable from any other type of said elements by elemental analysis. Each uniquely labeled support bears a multitude of similar or different oligonucleotides capable of hybridizing specifically to a particular target nucleic acid. [0015]Element tag" is a chemical moiety which includes an elemental atom or multitude of elemental atoms with one or many isotopes attached to a supporting molecular structure. The element tag also comprises the means of attaching the tag to a substrate, which can include (but is not limited to) pyrrole-2,5-dione(maleimido), sulfonic acid anion, or p-(chloromethyl)styrene (for thiol, N-terminus, or C-terminus, respectively). An elemental tag may be distinguishable from a multitude of other element tags in the same sample because its elemental or isotopic composition is different than that of the other tags. [0016]Transition element" means any element having the following atomic numbers, 2-29, 39-47, 57-79 and 89. Transition elements include the rare earth elements, lanthanides and noble metals. (Cotton and Wilkinson, 1972). [0017]An "affinity product" or "affinity reagent" refers to biological molecules (antibody, aptamer, lectin, sequence-specific binding peptide, etc) which are known to form highly specific non-covalent bonds with respective target molecules (peptides, antigens, small molecules, etc). Affinity reagent labeled with a unique element tag is an affinity product labeled with an element tag that is unique and distinguishable from a multitude of other element tags in the same sample. [0018]Hybridizes specifically to", refers to the binding, duplexing, or hybridizing of a nucleic acid molecule preferentially to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. Optimization of hybridization conditions is well known to those of skill in the art and are reviewed in WO95/219445. The term "stringent conditions" refers to conditions under which a probe will hybridize preferentially to its target subsequence, and to a lesser extent to, or not at all to, other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. Typically, stringent conditions will be those in which the salt concentration is at least about 0.01 to 1.0 M Na+ (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30.degree. C. for short probes (e.g., 10 to 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide, as is known to those skilled in the art. [0019]In situ hybridization" refers to a hybridization technique in which the hybridization reaction between the complementary single-stranded nucleic acid probe and endogenous target is carried out in specially prepared cells or histological sections without purification of target nucleic acid. [0020]Background signal intensity" refers to hybridization signals resulting from non-specific binding, or other interactions, between the target nucleic acids and labeled oligonucleotide (e.g., the oligonucleotide probes, control probes, etc.). Continue reading about Element-tagged olignucleotide gene expression analysis... Full patent description for Element-tagged olignucleotide gene expression analysis Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Element-tagged olignucleotide gene expression analysis patent application. Patent Applications in related categories: 20090291445 - Biomarker of lung injury and repair - The present invention resides in the discovery that circulating cytokaretin 5 (CK5) mRNA level correlates with the presence of a lung injury or disease as well as the severity or stage of the injury or disease. Diagnostic methods and kits are provided. ... 20090291450 - Caterpiller gene family - The present invention relates to a new family of structurally and functionally related nucleic acids and proteins, designed the CATERPILLER family, which is characterized by landmark structural motifs including a nucleotide binding domain and leucine-rich repeat domains. ... 20090291431 - Compositions and methods to detect legionella pneumophila nucleic acid - Compositions are disclosed as nucleic acid sequences that may be used as amplification oligomers, including primers, capture probes for sample preparation, and detection probes specific for Legionella pneumophila 16S or 23S rRNA sequences or DNA encoding 16S or 23S rRNA. Methods are disclosed for detecting the presence of L. pnuemophila ... 20090291433 - Droplet-based nucleic acid amplification method and apparatus - The present invention relates to a droplet-based nucleic acid amplification method and apparatus. According to one embodiment, a method of amplifying a nucleic acid in a biological sample is provided, wherein the method includes: (a) providing a system comprising a droplet microactuator electronically coupled to and controlled by a processor ... 20090291434 - Gene expression markers for colorectal cancer prognosis - A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject. ... 20090291432 - Genetic profiles associated with the 957c>t polymorphism in the drd2 gene - The present invention relates to a method for profiling an individual or group of individuals with respect to a neurological, psychiatric or psychological condition, phenotype or state, including a sub-threshold neurological, psychiatric or psychological condition, phenotype or state. More particularly, the present invention identifies a genetic profile associated with the ... 20090291442 - Hspa1a as a marker for sensitivity to ksp inhibitors - The present invention relates to methods for predicting a response to treatment with a kinesin spindle protein inhibitor using heat shock protein 70, isoform A1a, also known as HSPA1a, as a marker for sensitivity to the kinesin spindle protein (KSP) inhibitors. Method are provided for predicting a response to treatment ... 20090291449 - Method and apparatus to minimize diagnostic and other errors due to transposition of biological specimens among subjects - A method and apparatus for minimizing diagnostic errors due to transposition of biological specimens among subjects provides for independent biometric confirmation that a given specimen is from a given donor. In certain embodiments, a biological specimen confirmation kit comprises a portable and openable case housing components of the kit, at ... 20090291446 - Method for confirming the presence of an analyte - The invention provides methods and kits for the rapid confirmation of an initial analyte test result. In a preferred embodiment, the process confirms the presence of a given microbial target in a mixed culture, or a mixed enrichment media, even when the competing organisms in the mix belong to related ... 20090291440 - Method for synthesizing nucleic acid using dna polymerase beta and single molecule sequencing method - The present invention provides a nucleic acid synthesis method capable of continuously carrying out an extension reaction and a single molecule sequencing method capable of obtaining base information accurately at high speed. A method for synthesizing a nucleic acid, including the steps of: forming a complex of a target nucleic ... 20090291447 - Method of detecting colon cancer marker - It is intended to provide a non-invasive and convenient method of detecting a tumor marker for diagnosing colon cancer which is superior in sensitivity and specificity to the existing fecal occult blood test. More specifically speaking, a method of detecting a tumor marker for diagnosing colon cancer which comprises collecting ... 20090291444 - Methods and materials for detecting and treating dementia - This document relates to methods and materials involved in detecting mutations linked to dementia (e.g., frontotemporal lobar degeneration). For example, methods and materials for determining whether or not a mammal is homozygous for a mutant T allele of rs5848 are provided. This document also relates to methods and materials involved ... 20090291451 - Methods and primers for diagnosing idiopathic congenital central hypoventilation syndrome - The present invention provides assays and kits for diagnosing idiopathic congenital central hypoventilation syndrome. The present assays and kits focus on the second polyalanine repeat of the PHOX2b gene or gene product, which is normally 20 residues in length. A polyalanine repeat 25 to 33 residues in length is strongly ... 20090291438 - Methods for analysis of extracelluar rna species - The invention provides methods and kits for enabling quantitative or qualitative analysis of extracellular RNA species in non-cellular bodily fluids including plasma and serum to detect, infer, evaluate, or monitor cancer and other neoplasia or other diseases of interest. ... 20090291436 - Methods for detecting nucleic acids indicative of cancer - The invention provides methods for screening tissue or body fluid samples for nucleic acid indicia of cancer or precancer. ... 20090291437 - Methods for targeting quadruplex sequences - Provided are quadruplex nucleotide sequences and methods for identifying interacting molecules. ... 20090291452 - Micro-rna profiles associated with endometrial cancer development and response to cisplatin and doxorubicin chemotherapy - A method predicting of cancer chemoresponse of the population of cancer cells to the one or more chemotherapeutic agents. Our ability to treat patients with advanced stage and recurrent endometrial cancer is hampered by an incomplete understanding of the molecular basis of disease development and response to therapy. A novel ... 20090291439 - Phosphatases involved in the regulation of cardiomyocyte differentiation - (C) an amino acid sequence having at least 60% or more homology to the amino acid sequence of SEQ ID NO:2 and having cysteine at position 138, wherein a protein consisting of the amino acid sequence has a dual specificity phosphatase activity. (B) an amino acid sequence wherein one or several ... 20090291441 - Polypeptide, nucleic acid molecule encoding it and their uses - A polypeptide containing epitope of the amino acid sequence shown in SEQ ID NO:3 is provided, which is selected from the amino acid sequence of SEQ ID NO:3 and amino acids at 16-32 positions, amino acids at 1-30 positions, amino acids at 50-80 positions and amino acids at 17-200 positions ... 20090291448 - Prognostic and predictive gene signature for non-small cell lung cancer and adjuvant chemotherapy - The application provides methods of prognosing and classifying lung cancer patients into poor survival groups or good survival groups and for determining the benefit of adjuvant chemotherapy by way of a multigene signature. The application also includes kits and computer products for use in the methods of the application. ... 20090291435 - Thermal reaction device and method for using the same - Devices and methods for performing the relative concentration of a target in a sample, the sample containing both target and non-target components, the method performed by partitioning the sample into a large number of reaction volumes such that the target is concentrated relative to the non-target, and performing a detection ... 20090291443 - Use of highly parallel snp genotyping for fetal diagnosis - The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions. ... ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. Start now! - Receive info on patent apps like Element-tagged olignucleotide gene expression analysis or other areas of interest. ### Previous Patent Application: Methods of extracting nucleic acids Next Patent Application: Method for using biomaterials as reagent for nano-patterning Industry Class: Chemistry: molecular biology and microbiology ### FreshPatents.com Support Thank you for viewing the Element-tagged olignucleotide gene expression analysis patent info. IP-related news and info Results in 0.14162 seconds Other interesting Feshpatents.com categories: Accenture , Agouron Pharmaceuticals , Amgen , AT&T , Bausch & Lomb , Callaway Golf 174 |
 * Protect your Inventions * US Patent Office filing 
PATENT INFO |
|
