Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Gammaretrovirus: A genus of RETROVIRIDAE comprising endogenous sequences in mammals, related RETICULOENDOTHELIOSIS VIRUSES, AVIAN, and a reptilian virus. Many species contain oncogenes and cause leukemias and sarcomas.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Nucleic Acids: High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages.Peptide Nucleic Acids: DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Biotin: A water-soluble, enzyme co-factor present in minute amounts in every living cell. It occurs mainly bound to proteins or polypeptides and is abundant in liver, kidney, pancreas, yeast, and milk.Methods: A series of steps taken in order to conduct research.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Indicators and Reagents: Substances used for the detection, identification, analysis, etc. of chemical, biological, or pathologic processes or conditions. Indicators are substances that change in physical appearance, e.g., color, at or approaching the endpoint of a chemical titration, e.g., on the passage between acidity and alkalinity. Reagents are substances used for the detection or determination of another substance by chemical or microscopical means, especially analysis. Types of reagents are precipitants, solvents, oxidizers, reducers, fluxes, and colorimetric reagents. (From Grant & Hackh's Chemical Dictionary, 5th ed, p301, p499)In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Retroviridae: Family of RNA viruses that infects birds and mammals and encodes the enzyme reverse transcriptase. The family contains seven genera: DELTARETROVIRUS; LENTIVIRUS; RETROVIRUSES TYPE B, MAMMALIAN; ALPHARETROVIRUS; GAMMARETROVIRUS; RETROVIRUSES TYPE D; and SPUMAVIRUS. A key feature of retrovirus biology is the synthesis of a DNA copy of the genome which is integrated into cellular DNA. After integration it is sometimes not expressed but maintained in a latent state (PROVIRUSES).Fluorescent Dyes: Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.TritiumMolecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Genes, Viral: The functional hereditary units of VIRUSES.RNA-Directed DNA Polymerase: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Antigens, Viral: Substances elaborated by viruses that have antigenic activity.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Micropore Filters: A membrane or barrier with micrometer sized pores used for separation purification processes.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Cell Line: Established cell cultures that have the potential to propagate indefinitely.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Nucleic Acid Probes: Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Centrifugation, Density Gradient: Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Kinetics: The rate dynamics in chemical or physical systems.Herpesvirus 4, Human: The type species of LYMPHOCRYPTOVIRUS, subfamily GAMMAHERPESVIRINAE, infecting B-cells in humans. It is thought to be the causative agent of INFECTIOUS MONONUCLEOSIS and is strongly associated with oral hairy leukoplakia (LEUKOPLAKIA, HAIRY;), BURKITT LYMPHOMA; and other malignancies.Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.RNA Probes: RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.

*  Brevet US5853993 - Signal enhancement method and kit - Google Brevets

... whereby the hybridization of multiple reporter probes to the homopolymeric region provides for signal amplification; and (b) ... The invention discloses and claims a signal amplification method for detecting a target nucleic acid analyte having a ... Nucleic acid multimers and amplified nucleic acid hybridization assays using same. US5437977 *. 29 mai 1992. 1 ao t 1995. David ... The term "target nucleic acid analyte" refers to a nucleic acid whose presence or absence in a sample is desired to be detected ...

*  Patent US6777184 - Detection of nucleic acid hybridization by fluorescence polarization - Google Patents

... systems and assays are provided for FP detection of nucleic acid hybridization. ... Making Nucleic Acids. In the present invention, a probe nucleic acid is typically hybridized to a target nucleic acid. Either ... contacting a first nucleic acid to a second nucleic acid, which second nucleic acid comprises a neutral or positively charged ... contacting the target nucleic acid sequence with a labeled nucleic acid probe, which labeled nucleic acid probe comprises a ...,346,545

*  Patent US4599303 - Nucleic acid hybridization assay employing probes crosslinkable to target ... - Google Patents

Single stranded nucleic acid probes are employed which contain complementary base sequences to nucleic acid target molecules. ... of label in the crosslinked hybrid can be measured as an extremely sensitive method for assaying for specific nucleic acid ... Novel methods and reagents for determining the presence of specific nucleic acid base sequences by employing crosslinking ... Degradable nucleic acid probes and nucleic acid detection methods. US6652808 *. Dec 6, 1996. Nov 25, 2003. Nanotronics, Inc.. ...,371,548

*  Differentiation of bean-infecting geminiviruses by nucleic acid hybridization probes and aspects of bean golden mosaic in Brazil

Nucleic acid dot and squash blot methods were used to prepare samples for hybridization, and the dot blot method was used to ... Differentiation of bean-infecting geminiviruses by nucleic acid hybridization probes and aspects of bean golden mosaic in ... PHASEOLUS VULGARIS; BEAN GOLDEN MOSAIC VIRUS; DISEASE TRANSMISSION; HOMOPTERA; VECTORS; SYMPTOMATOLOGY; ANALYSIS; NUCLEIC ACIDS ... determine relative differences in viral nucleic acid titers in infected bean leaves. The general and specific probes were ...

*  Multiplexed Interfacial Transduction of Nucleic Acid Hybridization Using a Single Color of Immobilized Quantum Dot Donor and...

Multiplexed Interfacial Transduction of Nucleic Acid Hybridization Using a Single Color of Immobilized Quantum Dot Donor and ...

*  Sensors | Free Full-Text | Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes ...

... has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization ... Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer ... we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes ...

*  Microbiology - University Biological Sciences - Marked by

Nucleic acid hybridization After which the filter is incubated in a solution that contains the labelled probe in the ... Folic acid. In 1993 the Food and Drug Administration (FDA), in the USA suggested the regulation of fortification of folic acid ... It was synthesised by the Americans naming it the chemical name pteroylglutamic acid. Folic acid is water soluble therefore it ... After hybridisation, the filter is washed to remove the probe and the stringent of the washing can be altered so that only ...

*  What is the difference between mildew and mold? |

How do you describe the process of nucleic acid hybridization?. * Q: How do you kill black mold using vinegar?. ...



*  Patent US5541113 - Method for detecting an analyte using an electrochemical luminescent ... - Google Patents

Electrochemical detection of nucleic acid hybridization. US20020168699 *. Dec 14, 2001. Nov 14, 2002. Bechtel Bwxt Idaho, Llc. ... Electrochemical detection of nucleic acid hybridization. US20060057741 *. Apr 6, 2005. Mar 16, 2006. Thompson Vicki S. Rapid ... Electrochemical detection of nucleic acid hybridization. US6432722 *. Mar 15, 1999. Aug 13, 2002. Roche Diagnostics Gmbh. ... Microelectronic device for electrochemical detection of nucleic acid hybridization. US7150998. Dec 19, 2000. Dec 19, 2006. ...,403,220

*  Biological, biochemical and physicochemical evidence for the existence of the polyadenylate - polyuridylate - poly 2'-fluoro-2'...

Nucleic Acid Hybridization. Poly A / pharmacology. Poly U / pharmacology. Polynucleotides / pharmacology*. Rabbits. ...

*  Gene expression of human sperm component related to A4 amyloid precursor protein.

The partial cDNA encoding the protein was isolated from a rat testis lambda gt11 expression library and the amino acid sequence ... Nucleic Acid Hybridization. Protein Precursors / analysis, genetics*, metabolism. RNA Probes. RNA, Messenger / genetics. ... By an in situ hybridization technique the mRNA for the antigen was detected in germ cells at all stages of spermatogenesis. The ... The partial cDNA encoding the protein was isolated from a rat testis lambda gt11 expression library and the amino acid sequence ...

*  Transcription of the viral genome in cell lines transformed by simian virus 40. I. Mapping of virus-specific nuclear RNAs.

Nucleic Acid Hybridization. Nucleic Acid Renaturation. RNA, Viral / biosynthesis*. Rats. Simian virus 40 / metabolism*. ... Title: Nucleic acids research Volume: 8 ISSN: 0305-1048 ISO Abbreviation: Nucleic Acids Res. Publication Date: 1980 Jan ... Journal ID (nlm-ta): Nucleic Acids Res. ISSN: 0305-1048. ISSN: 1362-4962. Article Information. Download PDF Print publication ...

*  Search Results

Nucleic Acids: Subtractive Hybridization. Richard J Byers, Judith A Hoyland, Anthony J Freemont. Published online: May 2005. ... Nucleic Acid Hybridization. Sarah WL Chan, Andy KH Choo. Published online: September 2005. ...

*  Patent US8039271 - Assays employing randomly distributed microbeads with attached biomolecules - Google Patents

Solid supports for nucleic acid hybridization assays. US5516635. 15 Oct 1992. 14 May 1996. Ekins; Roger P.. Binding assay ... wherein at least one of said nucleic acids is a nucleic acid analog. ... Method for increasing the sensitivity of nucleic acid hybridization assays. EP0392546A2 *. 12 Apr 1990. 17 Oct 1990. Ro ... Detection of a nucleic acid sequence or a change therein. US5866331. 20 Oct 1995. 2 Feb 1999. University Of Massachusetts. ...

*  Patent US20040110439 - Native protein mimetic fibers, fiber networks and fabrics for medical use - Google Patents

I and II, IRL Press, Oxford, UK; Hames and Higgins (eds.) (1985) Nucleic Acid Hybridization, IRL Press, Oxford, UK; and Setlow ... 19A-19D are SEM micrographs of collagen-PEO (1:1) fibers spun from 2wt % acid solution at a flow rate of 100 μL/min and at ... 20A-20D are SEM micrographs of collagen-PEO (1:1 (w/w), 34 mM NaCl) fibers spun from 2 wt % acid solution at different flow ... Acid-soluble collagen was derived from tail tendons obtained from Sprague-Dawley rats weighing between 250 to 350 grams using a ...

*  Patent US6893824 - Gene detection system, gene detection device comprising same, detection ... - Google Patents

... whereby genes can be rapidly detected with high sensitivity through hybridization. ... A gene detection system for detecting a target gene upon hybridization with a probe comprising a probe-immobilizing support on ... Electrochemical assay for nucleic acids and nucleic acid probes. US4857831 *. Dec 29, 1986. Aug 15, 1989. Schlumberger ... peptidic nucleic acid, or LNA (locked nucleic acid; Proligo, a trademark of LLC). ...,825,352

*  Patent US7943374 - Super-size adeno-associated viral vector harboring a recombinant genome ... - Google Patents

I & II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., Current Edition); Nucleic Acid Hybridization (B. Hames & S. ... region of a nucleic acid composition is a segment of nucleic acid within or attached to another nucleic acid composition that ... Such techniques can be used to introduce one or more nucleic acid compositions, such as a plasmid vector and other nucleic acid ... I & II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., Current Edition); Nucleic Acid Hybridization (B. Hames & S. ...

*  Patent US20040043502 - Membrane-based assay devices that utilize time-resolved fluorescence - Google Patents

... including label and capture nucleic acid sequences used in DNA hybridization assays to detect a target nucleic acid sequence), ... Solid supports for nucleic acid hybridization assays. US5516635 *. 15 Oct 1992. 14 May 1996. Ekins; Roger P.. Binding assay ... Electrochemical detection of nucleic acid sequences. US6396053 *. 1 Nov 1999. 28 May 2002. Olympus Optical Co.. Scanning ... or a mixed ester of nitric acid and other acids, such as aliphatic carboxylic acids having from 1 to 7 carbon atoms. ...

*  Patent US4256834 - Fluorescent scavenger particle immunoassay - Google Patents

Method and kit for performing nucleic acid hybridization assays. WO1988004429A1 *. Dec 1, 1986. Jun 16, 1988. Burton James A. A ... Method and kit for performing nucleic acid hybridization assays. US5279937 *. Apr 30, 1992. Jan 18, 1994. Detechnology Canada. ... Selective isolation and concentration of nucleic acids from complex samples. US20070190551 *. Dec 8, 2006. Aug 16, 2007. ... For many ligands of interest, particularly large molecules, such as proteins, polysaccharides, nucleic acids, and the like, ...,633,076

*  KGI | Current Students | Academic Affairs | Course Catalog | ALS 320: Medical Diagnostics

Biomolecular recognition / nucleic acid hybridization. *Enzymes in clinical and molecular diagnostics. *Heat transfer of ...

*  Patent US4210722 - Protein immobilizer - Google Patents

Devices and methods for optical detection of nucleic acid hybridization. US6251278 *. Mar 3, 1999. Jun 26, 2001. Chromatochem, ... Devices and methods for optical detection of nucleic acid hybridization. EP0038960A2 *. Apr 3, 1981. Nov 4, 1981. Toray ... Agents and procedures for the transfer of proteins and/or nucleic acids onto a supported receptor surface. ... polymers containing acid residues, and the like. The support may have any shape and may include particulate or fibrous ...,832,511

*  Patent US6171804 - Method of determining interdomain orientation and changes of interdomain ... - Google Patents

1984); Nucleic Acid Hybridization [B. D. Hames & S. J. Higgins eds. (1985)]; Transcription And Translation [B. D. Hames & S. J ... nucleic acid binding site and the agent identified is a potential agonist or antagonist of the DNA binding protein-nucleic acid ... 1994). Nucleic acids encoding the selected protein portion (or domain) can be placed into an expression vector (e.g., pGEX2T) ... In still another embodiment the biopolymer is a nucleic acid such as a DNA, MRNA, ribosomal RNA or ribozyme. The polymer of the ...

*  Patent US5759776 - Targets for breast cancer diagnosis and treatment - Google Patents

Nucleic acid multimers and amplified nucleic acid hybridization assays using same. US5324654 *. Jan 8, 1992. Jun 28, 1994. The ... If desired, the nucleic acid may be extracted from the sample, and may also be partially purified. To measure gene duplication ... Process for amplifying, detecting, and/or-cloning nucleic acid sequences. US4683202 *. Oct 25, 1985. Nov 27, 1990. Cetus Corp. ... Nucleic acids and corresponding proteins entitled 273P4B7 useful in treatment and detection of cancer. ...

*  Methods for detecting Hepatitis C virus using polynucleotides specific for same - Chiron Corporation

In the basic nucleic acid hybridization assay, single-stranded analyte nucleic acid (either DNA or RNA) is hybridized to a ... 16, 1987). These publications describe a solution phase nucleic acid hybridization assay in which the analyte nucleic acid is ... The cDNA used as a template for the PCR reaction was derived from the nucleic acids (either total nucleic acids or RNA) ... Detection of Amplified HCV Nucleic Acid Sequences derived from HCV Nucleic. Acid Sequences in Liver and Plasma Specimens from ...

DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Hyperchromicity: Hyperchromicity is the increase of absorbance (optical density) of a material. The most famous example is the hyperchromicity of DNA that occurs when the DNA duplex is denatured.Nucleic acid secondary structure: The secondary structure of a nucleic acid molecule refers to the basepairing interactions within a single molecule or set of interacting molecules, and can be represented as a list of bases which are paired in a nucleic acid molecule.Q-FISH: Quantitative Fluorescent in situ hybridization (Q-FISH) is a cytogenetic technique based on the traditional FISH methodology. In Q-FISH, the technique uses labelled (Cy3 or FITC) synthetic DNA mimics called peptide nucleic acid (PNA) oligonucleotides to quantify target sequences in chromosomal DNA using fluorescent microscopy and analysis software.Allele-specific oligonucleotide: An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay.Biotin sulfoxideTransfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Fluorescent tag: In molecular biology and biotechnology, a fluorescent tag, also known as a label or probe, is a molecule that is attached chemically to aid in the labeling and detection of a biomolecule such as a protein, antibody, or amino acid. Generally, fluorescent tagging, or labeling, uses a reactive derivative of a fluorescent molecule known as a fluorophore.Tritium illumination: Tritium illumination is the use of gaseous tritium, a radioactive isotope of hydrogen, to create visible light. Tritium emits electrons through beta decay, and, when they interact with a phosphor material, fluorescent light is created, a process called radioluminescence.Coles PhillipsLigation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Thermal cyclerRestriction fragment: A restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site.Hybrid inviability: Hybrid inviability is a post-zygotic barrier, which reduces a hybrid's capacity to mature into a healthy, fit adult.Hybrid inviability.Lewis H. Brown: Lewis Brown}}Nucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.YjdF RNA motifPolymethine: Polymethines are compounds made up from an odd number of methine groups (CH) bound together by alternating single and double bonds.Kachovski and Dekhtyar, Dyes and Pigments, 22 (1983) 83-97 Compounds made up from an even number of methine groups are known as polyenes.Mature messenger RNA: Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, it consists exclusively of exons, with all introns removed.Polymerase-endonuclease amplification reaction: Polymerase-endonuclease amplification reaction (PEAR) is a DNA amplification technology for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI) cleavage releases monomeric duplex oligonucleotides.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Buoyant density ultracentrifugation: Buoyant density centrifugation uses the concept of buoyancy to separate molecules in solution. Usually a caesium chloride (CsCl) solution is used, but in the general case it's usually approximately the same density as the molecules that are to be centrifuged.Triparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.Assay sensitivity: Assay sensitivity is a property of a clinical trial defined as the ability of a trial to distinguish an effective treatment from a less effective or ineffective intervention. Without assay sensitivity, a trial is not internally valid and is not capable of comparing the efficacy of two interventions.Eukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Abscription: During normal transcription, RNA polymerase transcribes a number of short nonproductive oligonucleotides, and this process is called abortive transcription. The trapped RNAPs have been named abscriptases and the synthesis of specific length oligonucleotides called abscription.Fishpaper: Fish paper or fishpaper is a strong, flexible, fibrous dielectric paper. It resists moderate heat and mechanical injury, and is often used for wrapping coils and insulating stove-top parts.Permissive temperature: The permissive temperature is the temperature at which a temperature sensitive mutant gene product takes on a normal, functional phenotype.http://www.Burst kinetics: Burst kinetics is a form of enzyme kinetics that refers to an initial high velocity of enzymatic turnover when adding enzyme to substrate. This initial period of high velocity product formation is referred to as the "Burst Phase".Michael A. EpsteinRiboprobe: Riboprobes are RNA probes that can be produced by in vitro transcription of cloned DNA inserted in a suitable plasmid downstream of a viral promoter. Some bacterial viruses code for their own RNA polymerases, which are highly specific for the viral promoters.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.

(1/18626) Identification and characterization of the human orthologue of yeast Pex14p.

Pex14p is a central component of the peroxisomal protein import machinery, which has been suggested to provide the point of convergence for PTS1- and PTS2-dependent protein import in yeast cells. Here we describe the identification of a human peroxisome-associated protein (HsPex14p) which shows significant similarity to the yeast Pex14p. HsPex14p is a carbonate-resistant peroxisomal membrane protein with its C terminus exposed to the cytosol. The N terminus of the protein is not accessible to exogenously added antibodies or protease and thus might protrude into the peroxisomal lumen. HsPex14p overexpression leads to the decoration of tubular structures and mislocalization of peroxisomal catalase to the cytosol. HsPex14p binds the cytosolic receptor for the peroxisomal targeting signal 1 (PTS1), a result consistent with a function as a membrane receptor in peroxisomal protein import. Homo-oligomerization of HsPex14p or interaction of the protein with the PTS2-receptor or HsPex13p was not observed. This distinguishes the human Pex14p from its counterpart in yeast cells and thus supports recent data suggesting that not all aspects of peroxisomal protein import are conserved between yeasts and humans. The role of HsPex14p in mammalian peroxisome biogenesis makes HsPEX14 a candidate PBD gene for being responsible for an unrecognized complementation group of human peroxisome biogenesis disorders.  (+info)

(2/18626) The LIM-only protein PINCH directly interacts with integrin-linked kinase and is recruited to integrin-rich sites in spreading cells.

PINCH is a widely expressed and evolutionarily conserved protein comprising primarily five LIM domains, which are cysteine-rich consensus sequences implicated in mediating protein-protein interactions. We report here that PINCH is a binding protein for integrin-linked kinase (ILK), an intracellular serine/threonine protein kinase that plays important roles in the cell adhesion, growth factor, and Wnt signaling pathways. The interaction between ILK and PINCH has been consistently observed under a variety of experimental conditions. They have interacted in yeast two-hybrid assays, in solution, and in solid-phase-based binding assays. Furthermore, ILK, but not vinculin or focal adhesion kinase, has been coisolated with PINCH from mammalian cells by immunoaffinity chromatography, indicating that PINCH and ILK associate with each other in vivo. The PINCH-ILK interaction is mediated by the N-terminal-most LIM domain (LIM1, residues 1 to 70) of PINCH and multiple ankyrin (ANK) repeats located within the N-terminal domain (residues 1 to 163) of ILK. Additionally, biochemical studies indicate that ILK, through the interaction with PINCH, is capable of forming a ternary complex with Nck-2, an SH2/SH3-containing adapter protein implicated in growth factor receptor kinase and small GTPase signaling pathways. Finally, we have found that PINCH is concentrated in peripheral ruffles of cells spreading on fibronectin and have detected clusters of PINCH that are colocalized with the alpha5beta1 integrins. These results demonstrate a specific protein recognition mechanism utilizing a specific LIM domain and multiple ANK repeats and suggest that PINCH functions as an adapter protein connecting ILK and the integrins with components of growth factor receptor kinase and small GTPase signaling pathways.  (+info)

(3/18626) Isolation of human transcripts expressed in hamster cells from YACs by cDNA representational difference analysis.

Gene isolation methods used during positional cloning rely on physical contigs consisting of bacterial artificial chromosomes, P1, or cosmid clones. However, in most instances, the initial framework for physical mapping consists of contigs of yeast artificial chromosome (YACs), large vectors that are suboptimal substrates for gene isolation. Here we report a strategy to identify gene sequences contained within a YAC by using cDNA representational difference analysis (RDA) to directly isolate transcripts expressed from the YAC in mammalian cells. The RDA tester cDNAs were generated from a previously reported hamster cell line derived by stable transfer of a 590-kb YAC (911D5) that expressed NPC1, the human gene responsible for Niemann-Pick type C (NP-C). The driver cDNAs were generated from a control hamster cell line that did not contain the YAC that expressed NPC1. Among the gene fragments obtained by RDA, NPC1 was the most abundant product. In addition, two non-NPC1 fragments were isolated that were mapped to and expressed from 911D5. One of these RDA gene fragments (7-R) spans more than one exon and has 98% sequence identity with a human cDNA clone reported previously as an expressed sequence tag (EST), but not mapped to a chromosomal region. The other fragment (2-R) that had no significant sequence similarities with known mammalian genes or ESTs, was further localized to the region of overlap between YACs 911D5 and 844E3. The latter YAC is part of a contig across the NP-C candidate region, but does not contain NPC1. This two-part approach in which stable YAC transfer is followed by cDNA RDA should be a useful adjunct strategy to expedite the cloning of human genes when a YAC contig is available across a candidate interval.  (+info)

(4/18626) Single atom modification (O-->S) of tRNA confers ribosome binding.

Escherichia coli tRNALysSUU, as well as human tRNALys3SUU, has 2-thiouridine derivatives at wobble position 34 (s2U*34). Unlike the native tRNALysSUU, the full-length, unmodified transcript of human tRNALys3UUU and the unmodified tRNALys3UUU anticodon stem/loop (ASLLys3UUU) did not bind AAA- or AAG-programmed ribosomes. In contrast, the completely unmodified yeast tRNAPhe anticodon stem/loop (ASLPheGAA) had an affinity (Kd = 136+/-49 nM) similar to that of native yeast tRNAPheGmAA (Kd = 103+/-19 nM). We have found that the single, site-specific substitution of s2U34 for U34 to produce the modified ASLLysSUU was sufficient to restore ribosomal binding. The modified ASLLysSUU bound the ribosome with an affinity (Kd = 176+/-62 nM) comparable to that of native tRNALysSUU (Kd = 70+/-7 nM). Furthermore, in binding to the ribosome, the modified ASLLys3SUU produced the same 16S P-site tRNA footprint as did native E. coli tRNALysSUU, yeast tRNAPheGmAA, and the unmodified ASLPheGAA. The unmodified ASLLys3UUU had no footprint at all. Investigations of thermal stability and structure monitored by UV spectroscopy and NMR showed that the dynamic conformation of the loop of modified ASLLys3SUU was different from that of the unmodified ASLLysUUU, whereas the stems were isomorphous. Based on these and other data, we conclude that s2U34 in tRNALysSUU and in other s2U34-containing tRNAs is critical for generating an anticodon conformation that leads to effective codon interaction in all organisms. This is the first example of a single atom substitution (U34-->s2U34) that confers the property of ribosomal binding on an otherwise inactive tRNA.  (+info)

(5/18626) Suppression subtractive hybridization identifies high glucose levels as a stimulus for expression of connective tissue growth factor and other genes in human mesangial cells.

Accumulation of mesangial matrix is a pivotal event in the pathophysiology of diabetic nephropathy. The molecular triggers for matrix production are still being defined. Here, suppression subtractive hybridization identified 15 genes differentially induced when primary human mesangial cells are exposed to high glucose (30 mM versus 5 mM) in vitro. These genes included (a) known regulators of mesangial cell activation in diabetic nephropathy (fibronectin, caldesmon, thrombospondin, and plasminogen activator inhibitor-1), (b) novel genes, and (c) known genes whose induction by high glucose has not been reported. Prominent among the latter were genes encoding cytoskeleton-associated proteins and connective tissue growth factor (CTGF), a modulator of fibroblast matrix production. In parallel experiments, elevated CTGF mRNA levels were demonstrated in glomeruli of rats with streptozotocin-induced diabetic nephropathy. Mannitol provoked less mesangial cell CTGF expression in vitro than high glucose, excluding hyperosmolality as the key stimulus. The addition of recombinant CTGF to cultured mesangial cells enhanced expression of extracellular matrix proteins. High glucose stimulated expression of transforming growth factor beta1 (TGF-beta1), and addition of TGF-beta1 to mesangial cells triggered CTGF expression. CTGF expression induced by high glucose was partially suppressed by anti-TGF-beta1 antibody and by the protein kinase C inhibitor GF 109203X. Together, these data suggest that 1) high glucose stimulates mesangial CTGF expression by TGFbeta1-dependent and protein kinase C dependent pathways, and 2) CTGF may be a mediator of TGFbeta1-driven matrix production within a diabetic milieu.  (+info)

(6/18626) Human geranylgeranyl diphosphate synthase. cDNA cloning and expression.

Geranylgeranyl diphosphate (GGPP) synthase (GGPPSase) catalyzes the synthesis of GGPP, which is an important molecule responsible for the C20-prenylated protein biosynthesis and for the regulation of a nuclear hormone receptor (LXR.RXR). The human GGPPSase cDNA encodes a protein of 300 amino acids which shows 16% sequence identity with the known human farnesyl diphosphate (FPP) synthase (FPPSase). The GGPPSase expressed in Escherichia coli catalyzes the GGPP formation (240 nmol/min/mg) from FPP and isopentenyl diphosphate. The human GGPPSase behaves as an oligomeric molecule with 280 kDa on a gel filtration column and cross-reacts with an antibody directed against bovine brain GGPPSase, which differs immunochemically from bovine brain FPPSase. Northern blot analysis indicates the presence of two forms of the mRNA.  (+info)

(7/18626) The biosynthesis of transfer RNA in insects. II. Isolation of transfer RNA precursors from the posterior silk gland of Bombyx mori.

The occurrence of precursors to tRNA in the post-polysomal fraction of the posterior silk gland of Bombyx mori was demonstrated by pulse-chase labeling and DNA-RNA hybridization competition experiments. These precursors had molecular sizes ranging from 4S to 5S on polyacrylamide gel electrophoresis. Analysis of the incorporation of the methyl group from [methyl-14C]methionine revealed that a radioactive peak on polyacrylamide gel appeared in the 4.5S region during brief labeling. This suggested that some methylation occurred at the 4.5S precursor step.  (+info)

(8/18626) Burkholderia cocovenenans (van Damme et al. 1960) Gillis et al. 1995 and Burkholderia vandii Urakami et al. 1994 are junior synonyms of Burkholderia gladioli (Severini 1913) Yabuuchi et al. 1993 and Burkholderia plantarii (Azegami et al. 1987) Urakami et al. 1994, respectively.

Reference strains of Burkholderia cocovenenans and Burkholderia vandii were compared with strains of other Burkholderia species using SDS-PAGE of whole-cell proteins, DNA-DNA hybridization and extensive biochemical characterization. Burkholderia gladioli and B. cocovenenans were indistinguishable in the chemotaxonomic and biochemical analyses. Burkholderia plantarii and B. vandii had indistinguishable whole-cell protein patterns but the B. vandii type strain differed from B. plantarii strains in several biochemical tests. The DNA-DNA binding levels (higher than 70%) indicated that (i) B. gladioli and B. cocovenenans, and (ii) B. plantarii and B. vandii each represent a single species. It is concluded that B. cocovenenans and B. vandii are junior synonyms of B. gladioli and B. plantarii, respectively.  (+info)


  • Single stranded nucleic acid probes are employed which. (
  • Single stranded nucleic acid probes are employed which contain complementary base sequences to nucleic acid target molecules. (


  • 11. The method of claim 1 , wherein the first or second nucleic acids comprise at least a region which is single-stranded. (
  • labeled crosslinking molecules attached to said single-stranded nucleic acid molecules which are capable of forming covalent crosslinks between said single stranded nucleic acid molecules and said target molecules, whereby the presence of said specific nucleic acid base sequence is determined by measuring the amount of labeled probe covalently bound. (


  • A gene detection system for detecting a target gene upon hybridization with a probe comprising a probe-immobilizing support on which a probe is immobilized, and heating and cooling means disposed in contact with another location different from the surface of the probe-immobilizing support on which the probe is immobilized, whereby genes can be rapidly detected with high sensitivity through hybridization. (


  • 13. The method of claim 11 , wherein the first and second nucleic acid comprise at least one non-complementary nucleotide when aligned for maximum complementarity. (
  • 8. A method according to claim 7 , wherein all of said bioactive agents comprise nucleic acids. (


  • Novel methods and reagents for determining the presence of specific nucleic acid base sequences by employing crosslinking reactions of unique molecules capable of forming covalent bonds which are bonded with various labels or ligands for amplication. (
  • 5. The method according to claim 4 , wherein said identifier binding ligands are nucleic acids. (
  • 6. A method according to claim 5 , wherein said decoder binding ligands are nucleic acid and hybridize with said identifier binding ligands. (
  • 10. The method according to claim 9 , whereby said decoder binding ligands are nucleic acids and hybridize with said bioactive agents. (


  • and, detecting fluorescence polarization of the resulting mixture of first and second nucleic acids, wherein the fluorescence polarization is increased by less than about 50% by the addition of polylysine to the first and second nucleic acid. (
  • 3. The method of claim 1 , wherein the mixture of first and second nucleic acids is present in a composition which is substantially free of polyion. (
  • 5. The method of claim 1 , wherein a rotational diffusion rate of a duplex of the first and second nucleic acid is less than a rotational diffusion rate of the first or second nucleic acid. (
  • 6. The method of claim 5 , wherein the fluorescence polarization of unduplexed first or second nucleic acid is at least 50% different than the fluorescence polarization of the duplexed nucleic acid. (
  • 7. The method of claim 1 , wherein the first or second nucleic acid comprises one or more of: DNA, RNA, LNA, a DNA analogue, an RNA analogue or a PNA. (
  • 8. The method of claim 1 , wherein one or more of the nucleic acids is nuclease resistant. (
  • 10. The method of claim 1 , wherein the first nucleic acid is a DNA and the second nucleic acid is a PNA which comprises a rhodamine label. (
  • 12. The method of claim 11 , wherein the first and second nucleic acid are perfectly complementary. (
  • 16. The method of claim 1 , wherein the first and second nucleic acids hybridize in solution prior to detection of fluorescence polarization. (
  • 19. The method of claim 18 , wherein the third nucleic acid is perfectly complementary to either the first or the second nucleic acid. (
  • 7. A method according to claim 1 , wherein at least one of said bioactive agents comprises a nucleic acid. (
  • 9. A method according to claim 8 , wherein at least one of said nucleic acids is a nucleic acid analog. (


  • Methods, systems and assays are provided for FP detection of nucleic acid hybridization. (
  • 14. The method of claim 11 , further comprising determining from the fluorescence polarization detection whether the first and second nucleic acids are duplexed. (
  • 15. The method of claim 11 , further comprising determining the extent to which the first and second nucleic acids are duplexed from the fluorescence polarization detection. (
  • A gene detection system for detecting a target gene upon hybridization with a probe comprising a probe-immobilizing support on which a probe is immobilized, and heating and cooling means disposed in contact with another location different from the surface of the probe-immobilizing support on which the. (


  • By first hybridizing and then forming covalent bonds between the probe and target the amount of label in the crosslinked hybrid can be measured as an extremely sensitive method for assaying for specific nucleic acid sequences. (


  • 17. The method of claim 16 , comprising comparing the detected fluorescence polarization to a fluorescence polarization measurement of either the first or the second nucleic acid alone in solution. (
  • 18. The method of claim 16 , comprising comparing the detected fluorescence polarization to a fluorescence polarization measurement of either the first or the second nucleic acid hybridized to a third nucleic acid. (
  • 22. The method of claim 16 , comprising detecting fluorescence polarization during hybridization of the first and second nucleic acid. (
  • 23. The method of claim 22 , further comprising determining the fluorescence polarization as a function of time during hybridization of the first and second nucleic acid. (