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Topic: Hybridization probe

	In situ hybridization
		Hybridization buffer for oligonucleotide probes: 100 µg/ml autoclaved salmon sperm DNA, 50 µg/ml heparin, 0.1% Tween 20, and appropriate concentrations of formamide and SSC as described in section III D.-
		The pellet is washed in 70% ethanol, dried, and resuspended in 300 µl of hybridization buffer.
		Oligonucleotide probes are used at a concentration of 0.5 µg/ml.
	www.dartmouth.edu /~ambros/protocols/other/in_situ_hybrid_protocol.html (3529 words)

	Hybridization assay using self-quenching fluorescence probe - Patent 5876930 (Site not responding. Last check: 2007-11-03)
		During amplification, the probe is digested by the nuclease activity of a polymerase when hybridized to the target sequence to cause the fluorescent molecule to be separated from the quencher molecule, thereby causing fluorescence from the reporter molecule to appear.
		Since the reporter molecule on the probe exhibits a greater fluorescence signal when hybridized to a target sequence, an increase in the fluorescence signal after the probe is contacted with the sample indicates the hybridization of the probe to target sequences in the sample, thereby indicating the pressure of target sequences in the sample.
		Since the reporter molecule on the probe exhibits a greater fluorescence signal when hybridized to a target sequence, an increase in the fluorescence signal after the probe is contacted with the sample indicates the hybridization of the probe to target sequences in the sample and hence the presence of target sequences in the sample.
	www.freepatentsonline.com /5876930.html (9954 words)

	Hybridization method of detecting nucleic acid sequences with probe containing thionucleotide - Patent 4647529
		A hybridization probe constructed to contain thionucleotides is hybridized to a nucleotide sequence of interest in the absence of formamide, DTT and dextran sulfate.
		The hybridization technique is of prime importance in basic research directed at understanding the relationship between nucleotide sequences and their function, as well as in diagnostic use to detect known aberrant genes or disease agents such as viruses or bacteria.
		Hybridization was conducted as before, with the mass of bound lambda DNA being calculated from the observed cpm in the high energy.sup.32 P channel (the.sup.35 S emissions are less energetic and do not contribute at all to counts measured at this energy level).
	www.freepatentsonline.com /4647529.html (7980 words)

	Reference.com/Encyclopedia/Hybridization probe
		In molecular biology, a hybridization probe is a fragment of DNA of variable length (usually 100-1000 bases long), which is used to detect in DNA or RNA samples the presence of nucleotide sequences that are complementary to the sequence in the probe.
		The labeled probe is then denatured (by heating) into single DNA strands and hybridized to target DNA (Southern blotting) or RNA (northern blotting) immobilized on a membrane or in situ.
		Hybridization probes used in DNA microarrays refer to DNA covalently attached to an inert surface, such as coated glass slides or gene chips, and to which a mobile DNA target is hybridized.
	www.reference.com /browse/wiki/Hybridization_probe (210 words)

	Hybridization probe - Wikipedia, the free encyclopedia
		A hybridization probe is a short piece of DNA (on the order of 100-500 bases) that is denatured (by heating) into single strands and then radioactively labeled, usually with phosphorus (32P or 33P).
		The probe can be used in a Northern or Southern blot to detect genes or RNA transcripts with which it has homology (a region with similar base pair sequence).
		The location of the hybridization probe on the blot can then be determined by creating an image by exposing the hybridized blot to a phosphorus screen (similar to developing an x-ray image).
	en.wikipedia.org /wiki/Hybridization_probe (233 words)

	BioMed Central \| Full text \| Outliers involving the Poly(A) effect among highly-expressed genes in microarrays
		Hybridization intensity from oligo(dT) probe, as a function of the length of the clone insert for different microarray spots Oligo(dT) was end labeled with T4 kinase, then hybridized to a microarray.
		Hybridization intensity from oligo(dT) probe, as a function of the fraction of bases that are within a sequence run of AAAAAAA Oligo(dT) was end labeled with T4 kinase, then hybridized to a microarray.
		Hybridization of the membrane with radioactive cDNA was performed by the procedures described at http://www.resgen.com/gf200pro.html webcite, except that the last room temperature wash was performed in 2X SSC.
	www.biomedcentral.com /1471-2164/3/35 (5288 words)

	In Situ Hybridization
		Some disadvantages of oligonucleotide probes are that due to the process of oligonucleotide generation the labeling methods are limited, limitations on label quantity per probes leads to reduced sensitivity, and the hybrids are less stable because of the short length of the probes.
		After hybridization with a radioactive probe, the distribution of hybridized probe is detected by either opposing the tissue section slides to X-ray film or by dipping the slides in photographic emulsion.
		Hybridization is performed by placing a small amount of solution containing the hybridization probe on a cover slip, which is then placed on the slide containing tissue sections to incubate overnight.
	osiris.rutgers.edu /~smm/in_situ_hybridization.htm (3500 words)

	Millipore - Blotting Optimization -- Nylon Blotting Transfer Membranes for Nucleic Acid Applications
		The accessibility of the probe to the target during hybridization and the physical retention of the target on the membrane surface are two important parameters that must be balanced to achieve optimal hybridization.
		Probes, such as DNA or RNA fragments that have a sequence complementary to the target sequence, are hybridized to the target band on the membrane.
		In these instances, the probe may be directly labeled with hapten molecules to facilitate subsequent binding of a fluorescently-labeled secondary probe molecule and then visualized by detecting the secondary probe molecule.
	www.millipore.com /publications.nsf/docs/WWW1 (2624 words)

	FISH guide - hybridization buffers
		Two types of hybridization buffer, one regular and one concentrated, were prepared in our laboratory and were used to resuspend all labeled DNA probes (Table 6).
		New hybridization buffers prepared in the laboratory need needs to be tested for their performance.
		Although hybridization of a cosmid probe worked in all three cases, signal to noise ratio was much better in Fig.7g than in the first two pictures.
	info.med.yale.edu /genetics/ward/tavi/fi05.html (485 words)

	Dna Probes \| World of Genetics
		In practice, the probe and single stranded DNA from a mixture of cells or clone to be tested are mixed together.
		Hybridization occurs with the formation of stable bonds between the DNA of only one specific type of cell or clone in the section where its nucleotides are complementary with the probe.
		The main advantage of DNA probes are that they give fast, simple diagnostic tests for gene sequences in plant, animal, microbial and viral cells on the basis of the highly specific nucleotide sequence which differentiates on organism from another.
	www.bookrags.com /research/dna-probes-wog (849 words)

	Nucleic acid hybridization assays using cloned DNA probes to screen uncloned nucleic acid populations
		An important application of Southern blot hybridization in mammalian genetics is the ability to identify a given DNA probe as a member of a repetitive DNA family.
		Southern blot hybridization has been used extensively in molecular genetic studies as a means of genomic restriction mapping: a labeled DNA probe from one genome can be used to infer the structure of related sequences in the same or different genomes.
		Although double-stranded cDNAs have been used as probes, single-stranded complementary RNA probes (riboprobes) are preferred: the sensitivity of initially single-stranded probes is generally higher than that of double-stranded probes, presumably because a proportion of the denatured double-stranded probe renatures to form probe homoduplexes.
	www.ncbi.nlm.nih.gov /books/bv.fcgi?rid=hmg.section.508 (2436 words)

	situ hybridization (Site not responding. Last check: 2007-11-03)
		Therefore, in order to probe the tissue or cells of interest one has to increase the permeability of the cell and the visibility of the nucleotide sequence to the probe without destroying the structural integrity of the cell or tissue.
		Specificity of binding of oligonucleotide probes to the target gene in tissue sections with in situ hybridization can be further strengthened with the use and comparison of binding of two probes complementary to different regions within the given target gene in any given experiment.
		However with this method there is the strong possibility especially with short oligonucleotide probes of causing significant disruption of the hybridization of the probe to the target sequence in the tissue.
	www.genedetect.com /insitu.htm (5160 words)

	Principles of nucleic acid hybridization
		However, it is the annealing of a probe DNA strand and a complementary target DNA strand to form a labeled probe-target heteroduplex that defines the usefulness of a nucleic acid hybridization assay.
		The rationale of the hybridization assay is to use the identified probe to query the target DNA by identifying fragments in the complex target which may be related in sequence to the probe (Figure 5.8).
		Denaturation of double-stranded probe DNA is generally achieved by heating a solution of the labeled DNA to a temperature which disrupts the hydrogen bonds that hold the two complementary DNA strands together.
	www.ncbi.nlm.nih.gov /books/bv.fcgi?rid=hmg.section.484 (1604 words)

	Hybridization Potential (HP) calculator (Site not responding. Last check: 2007-11-03)
		The hybridization potential (HP) calculator determines the maximum HP for a probe and target sequence by simulating all potential hybridizations between a probe and a target sequence and is based on the principles outlined by Brunk et al.
		Briefly, the HP of a probe and target sequence can be calculated by multiplying the number of complementary G- or C-nucleotides by 3, the number of complementary A- or T-nucleotides by 2, and dividing the sum of these products by the number of nucleotides in the probe.
		For example, the sum of weighting factors for an A-nucleotide in a target and a T-nucleotide in a probe is 1 (0.5 + 0.5 = 1), therefore the relative contribution of this pair to the HP calculation of the probe-target duplex is 2 (2 x 1 = 2).
	stahl.ce.washington.edu /readmes/HP.readme.html (1007 words)

	Guoping Shu et al.
		Recently nonradiactive, high-throughput in situ hybridization has been proposed to monitor expression of a large number of genes in a multiple tissue array on a single glass slide in animals (9, 10).
		Since many factors such as, probe quality, plant tissue fixation, prehybridization tissue treatment, hybridization condition and hybridization buffer compositions, and stringency of post-hybridization washing, all affect the outcome, optimization of these parameters is often a time-consuming, and frustrating process.
		The ratio of probe and hybridization medium, called dilution ratio, should be strictly controlled since the final salt concentration on slide is critical for proper probe/target mRNA annealing.
	www.epress.com /w3jbio/vol4/shu/paper.htm (4224 words)

	Probe - Wikipedia, the free encyclopedia
		A robotic probe is a device that uses onboard instruments to gather and relay a variety of telemetry to controllers from remote, hazardous or otherwise difficult to reach locations.
		Probes may return their data over radio links or be physically tethered to controllers or another device, or to collect and return physical samples.
		A hybridization probe and chemical probe are used in molecular biology.
	en.wikipedia.org /wiki/Probe (452 words)

	[No title] (Site not responding. Last check: 2007-11-03)
		In situ hybridization, as the name suggests, is a method of localizing, either mRNA within the cytoplasm or DNA within the chromosomes of the nucleus, by hybridizing the sequence of interest to a complimentary strand of a nucleotide probe.
		Normal hybridization requires the isolation of DNA or RNA, separating it on a gel, blotting it onto nitrocellulose and probing it with a complimentary sequence.
		In situ hybridization presents a unique set of problems as the sequence to be detected will be at a lower concentration, be masked because of associated protein, or protected within a cell or cellular structure.
	martin.parasitology.mcgill.ca /insituhybridization/insitu.htm (5241 words)

	FDA/CFSAN BAM - Identification of Foodborne Bacterial Pathogens by Gene Probes
		The labeled probe DNA that fails to reform the double helix is removed by washing the probe-target complexes on the support at an appropriate temperature and salt concentration.
		Probes to specific determinants of virulence are useful in assessing a risk to public health posed by bacterial contamination.
		The reliability of the colony hybridization technique with oligonucleotide probes was tested by collaborative study, using pure cultures of strains harboring the STH or STP genes (36).
	www.cfsan.fda.gov /~ebam/bam-24.html (10806 words)

	DVA Concepts in Molecular Medicine: Course Outline, Part II (Site not responding. Last check: 2007-11-03)
		Once a hybridization signal is obtained it would be appropriate to go back and then optimize the signal by again testing various concentrations of proteinase K. One of the biggest problems with the technique as mentioned earlier is keeping the sections on the slide throughout the hybridization procedure.
		The specificity of the hybridization is indicated when one probe, VWF for example, hybridizes to endothelial cells and another probe hybridizes to other cells in serial sections (Wilcox et al 1988).
		Anytime the hybridization is pushed by increasing the probe concentration too high or by dropping the stringency of the final wash the first thing that happens is that all of the cells in the section show a nuclear signal.
	www.emory.edu /WILCOX/DVApart2.html (4219 words)

	FAQ: Probe Preparation and Hybridization on Biodyne® Nylon Membranes
		Hybridization solutions containing probe can often be re-used if the second test is within two days of the original preparation.
		Hybridization temperature is determined by the length of the probes structure.
		As with hybridization, stringency is controlled by salt concentration, surfactant concentration, temperature and the duration of the wash. Typically, there are two stages of stringency washes.
	www.pall.com /34696_28301.asp (736 words)

	Development and Clinical Evaluation of a Highly Sensitive PCR-Reverse Hybridization Line Probe Assay for Detection and ...
		with HPV type-specific probes (14, 19), type-specific PCR
		HPV-74 is identified by the probes 56/74 and 74.
		Human papillomavirus testing by hybrid capture appears to be useful in triaging women with a cytologic diagnosis of atypical squamous cells of undetermined significance.
	jcm.asm.org /cgi/content/full/37/8/2508 (6360 words)

	Criteria
		An ideal way to determine the specificity of a potential probe would be to generate alignments with other transcripts and score them using a system based on the Gibbs energy of hybridization.
		Additionally, since microarrays involve hybridizing many probes in parallel, there should be uniformity in the thermodynamics of probe hybridization across the chip.
		If it is, add this probe to the list of probes and jump the set number of bases toward the 5’ end before examining another potential probe.
	arep.med.harvard.edu /oligoprobes/choose_description.html (901 words)

	In Situ Hybridization (Site not responding. Last check: 2007-11-03)
		The probe for hybridization has been tagged with moieties (biotin, digoxigenin, dinitrophenol) that can be recognized by specific proteins (avidin, antibodies).
		At right are diagrammed the results of three different hybridization regimes: a 1kbp cloned probe containing an exon of a single copy gene (left); a 40kbp probe encompassing A (middle); the same probe, but with an excess of unlabeled highly repetitive DNA from the target species (right).
		The use of large DNA probes is complicated by the interspersion of highly repeated DNA among gene sequences in many species.
	opbs.okstate.edu /~melcher/MG/MGW1/MG1225.html (250 words)

	Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates -- Kellner et al. 15 ...
		A graph of the fraction of probe–target pairs that yielded a positive hybridization signal for a given number of probe–target sequence mismatches is indicated.
		In the case of marmoset, shrew, and armadillo, probe specificity as measured by analysis of sequenced BAC clones was slightly higher than that of the probes themselves.
		Since multiple linked probes were included in the test set of probes, in these species many clones were positive for more than one probe and therefore facilitated a more accurate selection of orthologous versus nonorthologous clones for sequencing.
	www.genome.org /cgi/content/full/15/1/166 (5599 words)

	Isolation of a cDNA Clone for the Human HLA-DR Antigen alpha Chain by Using a Synthetic Oligonucleotide as a ...
		We have used a synthetic 20-nucleotide hybridization probe to isolate a cDNA clone encoding the
		The cDNA clone isolated by this procedure is 1,100 nucleotides long; the nucleotide sequence of the 5' end of the cDNA insert corresponds to the amino acid sequence of the HLA-DR chain.
		Hybridization of this cDNA clone to genomic blots suggests that the HLA-DR chain is encoded by a single-copy gene.
	www.pnas.org /cgi/content/abstract/79/19/5966 (338 words)

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