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Topic: DNA hybridization

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	Recombinant DNA Technology
		DNA fragments that have been cut with REs can be separated based on their relative sizes by running them in a gel made of the polymer agarose, a jelly-like substance.
		DNA, which overall has a negative charge, is loaded into a well and current that runs from the negative to the positive poles is applied.
		The mixture is heated to separate the strands of double-stranded DNA containing the target sequence and then cooled to allow (1) the primers to find and bind to their complementary sequences on the separated strands and (2) the polymerase to extend the primers into new complementary strands.
	darwin.nmsu.edu /~molbio/mcb520/lecture2.html (2847 words)

	Millipore - Technical Library - Optimization of DNA Fixation to Immobilon-Ny+ Using Ultraviolet Light
		Hybridized probe DNA was stripped from the blots by incubation in 0.4 M NaOH for 30 min at 45°C with gentle agitation.
		DNA retention increased to a maximum of 63% at 60,000 uJoules/cm2 and decreased gradually to 58% at 200,000 uJoules/cm2.
		Effective hybridization of a nucleic acid probe to membrane-bound DNA is dependent on three factors: binding of the target DNA to the membrane during blotting, retention of the target DNA during hybridization and stringency washes, and accessibility of the target DNA to the probe molecule.
	www.millipore.com /publications.nsf/docs/tn054 (3155 words)

	Anatomy of a Comparative Gene Expression Study
		The reporters currently used in comparative hybridization to microarrays are fluorescent dyes (fluors), represented by the red and green circles attached to the cDNA's in the diagram [2].
		The DNA in the spots is bonded to the glass to keep it from washing off during the hybridization reaction.
		Both types of DNA have been used before in array-like applications: cDNA libraries were used for comparative hybridization before the advent of fluorescent microarrays, while oligonucleotide arrays are available commercially today from Affymetrix Corporation for rapid resequencing of a few genes important to AIDS and some cancers.
	www.cs.wustl.edu /~jbuhler/research/array (2945 words)

	Southerns, Northerns, Westerns, & Cloning: Molecular Searching Techniques (Site not responding. Last check: )
		DNA is first cut with restriction enzymes and the resulting double-stranded DNA fragments have an extended rod conformation without pre-treatment.
		After hybrids have formed between the probe and target, it is necessary to remove any probe that is on the filter that is not stuck to the target molecules.
		If we were to cut human DNA with a restriction enzyme and run it on a Southern blot probed with a clone of the actin gene from an other organism, we could construct a restriction map of the human actin gene.
	web.mit.edu /esgbio/www/rdna/rdna.html (3119 words)

	Differential Adhesion of Microspheres Mediated by DNA Hybridization I: Experiment Biophysical Journal - Find Articles
		The adhesiveness of microspheres depends on the strength of interaction between DNA chains on the bead and substrate surfaces, which is a function of the degree of DNA chain overlap, the fidelity of the match between hybridizing pairs, and other factors that affect the hybridization energy, such as the salt concentration in the hybridization buffer.
		Hybridization analysis involves detecting the signal generated by the binding of fluorescently labeled probe DNA or RNA sequences, and comparing the fluorescent intensities with those of the reference sample (23).
		Hybridization efficiency determined from this comparison is correlated to the concentration of specific nucleotides in sample and their chemistry.
	findarticles.com /p/articles/mi_qa3938/is_200606/ai_n16452349 (1027 words)

	The Yale DNA Hybridization Scandal: Introduction
		DNA hybridization is based on the idea that evolution represents the accumulation of DNA point mutations in different bio-historical lineages.
		This DNA is a hybrid, or heteroduplex, composed of one strand from each of two species.
		Different DNA preparations may melt at slightly different temperatures due to the way in which they are prepared, so each batch of hybridizations is subtracted specifically from the homoduplex it was carried out with.
	digilander.libero.it /avifauna/classificazione/sequence6.htm (2404 words)

	DNA hybridization - Wikipedia, the free encyclopedia
		Hybridization is the process of combining complementary, single-stranded nucleic acids into a single molecule.
		The DNA is digested with a restriction enzyme and the fragments are separated by electrophoresis.
		The gel is then overlaid with a nitrocellulose filter, to which the DNA fragments are transferred (blotting) to yield a replica of the gel.
	en.wikipedia.org /wiki/Hybridisation_(molecular_biology) (483 words)

	DNA Hybridization Analysis in Microfluidic Devices
		Hybridization analysis of nucleic acids using arrays of immobilized oligonucleotides or cDNAs is being developed in a number of laboratories for applications including gene mapping, detection of genetic diseases, and monitoring mRNA expression levels.
		In the present study, DNA probes were immobilized in the channels of a planar glass microfluidic device and exposed to unlabeled complementary or noncomplementary target sequences.
		Hybridization was determined using a dsDNA-specific intercalating fluorescent dye and fluorescence microscopy with CCD imaging.
	www.ornl.gov /sci/lsm/dnahyb.html (717 words)

	Taxonomy: Classifying Life
		The total DNA is extracted from the cells of each species and purified.
		DNA is much easier to sequence than protein.
		DNA is more stable than protein in the environment.
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/T/Taxonomy.html (3528 words)

	DNA hybridization
		The technique was called DNA hybridization, and they had been applying it extensively to problems of avian phylogeny already.
		Thus, if we wish to chop up and compare this DNA region of the human with that of the gorilla, as DNA hybridization does, each gene will in fact be fairly similar to no less than 7 genes in the other species.
		It thus becomes more difficult to separate the information on orthologous DNA divergence (which one is presumably interested in, in studying the evolution of taxa) from paralogous DNA divergence (which is the evolution of gene families, interesting in itself, but not here).
	personal.uncc.edu /jmarks/dnahyb/Dnahyb2.html (2693 words)

	DNA Hybridization by Meredith Spann
		One of the most useful of the purposes, however, is the use of DNA hybridization as a comparison technique which uses complementary base pairing to compare the genomes of two different species and evaluate the similarities between them.
		Although the technique of hybridization varies due to the differing properties of DNA molecules, the general technique involves a heating to denature the DNA helices, a cooling, and an incubation for a period of time (Karp 429).
		A different hybrid results from each mixture; either a "homoduplex" (the tracer and driver species being the same) or a "heteroduplex" (each strand of the duplex is from a different species.) Following this procedure, the tracer-driver mixtures are boiled for five minutes (Sibley 4).
	www.samford.edu /~gekeller/spann.html (1105 words)

	DNA hybridization bibliography
		Here we outlined the potential problems with DNA hybridization, showed that the data do not in fact seem to resolve the trichotomy for they subsume a great deal more variability in measurement than Sibley and Ahlquist had reported, and inferred the existence of unreported data alterations.
		Sibley, Charles G., Comstock, John A., and Ahlquist, Jon E. (1990) DNA hybridization evidence of hominoid phylogeny: A reanalysis of the data.
		It turns out that that this "correction" (based on a measurement of mean DNA length in an agarose gel, to the nearest single nucleotide, of whole genomic DNA, after sonication, labelling, incubation, and S1 nuclease digestion) is entirely responsible for the reciprocity, the resolution, and the claimed match to the (published, altered, non-comparable) Sibley numbers.
	personal.uncc.edu /jmarks/dnahyb/Biblio.html (4481 words)

	Biomems
		DNA are maybe prepared from a wide variety of samples such as tissue, bacteria, saliva, etc. For genotyping analysis, the sample is genomic DNA.
		The output consists of series of hybridization events, indicating the presence or the relative abundance of specific DNA sequences that are present in the sample.
		On the left, hybridization of ssDNA without the enzyme label is used as a reference point (normalized to 1), and on the right, with amplification, an impedance change of more than a factor 10 is observed.
	mmadou.eng.uci.edu /Research/DNA.htm (1523 words)

	Recombinant DNA Technology
		One common way is to isolate the plasmid DNA from several colonies, digest it with restriction enzymes that you know should cut the DNA at specific places, then run the DNA on an electrophoresis gel to see if the pieces are the proper sizes.
		DNA polymerase adds new bases to the 3' ends of the primers to create the new second strand.
		Uses DNA polymerase to synthesize a second DNA strand that is labeled.
	www.bios.niu.edu /johns/humgen/Recomb_DNA.htm (2028 words)

	Nucleic Acid Hybridizations
		The hybridization of a radioactive probe to filter bound DNA or RNA is one of the most informative experiments that is performed in molecular genetics.
		First a non-stringent wash is performed to remove the non-specifically bound DNA and the second wash is performed at a higher stringency that only permits highly homologous sequences to remain bound to the filter.
		Southern hybridization analysis can also be performed to determine if a phenotypic mutation is due to a structural change in the gene controlling the trait of interest.
	www.ndsu.nodak.edu /instruct/mcclean/plsc731/dna/dna6.htm (1396 words)

	DNA HYBRIDIZATION
		Approximately 10 ml of hybridization solution is used for one to a few filters per bag.
		Cloned DNA blots may be prehybridized as above, but usually background is low enough to skip this step.
		Place filters in a bag, add 65°C hybridization solution, heat the bag to 65°C in an oven or water bath and inject heat denatured probe.
	omrf.ouhsc.edu /~frank/DNAHYBRD.html (711 words)

	LMDp protocol: Southern blot hybridization
		The primer-template complex is a substrate for the "Klenow" fragment of DNA polymerase I. By substituting a radiolabeled nucleotide for a non-radioactive equivalent in the reaction mixture, newly synthesized DNA is radioactively labeled.
		The absence of the 5'-3' exonuclease activity associated with DNA polymerase I ensures that labeled nucleotides incorporated by the polymerase are not subsequently removed as mono-phosphates.
		The probe DNA is separated from the unincorporated nucleotides using a Sephadex G50-column.
	www.dmd.nl /protocol/DNAhybridization_ALG005.html (3115 words)

	Encoding Choices for Error Resistant DNA Computers.
		Though double stranded DNA appears to be a good, stable storage medium for information, most proposed DNA computation systems use single stranded DNA (oligonucleotides) for storage (and computation).
		Hybridization is the action of one oligonucleotide annealing to its complement.
		DNA is a stable molecule suitable for storage of large amounts of information.
	www.csd.uwo.ca /~morey/dnatalk/kevin/dna/dnaerror.html (1671 words)

	Non-Radioactive DNA Hybridization Experiments for the Undergraduate Laboratory: The Southern Blot Analysis
		The biotin-labeled DNA probe hybridizes with its complementary sequences on the Southern blot.
		Following the hybridization of probe with the Southern blot and washes to remove excess probe (step 9), the blot may be dried and stored at room temperature until the time to begin Experiment 8.
		A hybridization probe may be made by digesting pBR325 DNA with restriction enzymes and then isolating a particular restriction endonuclease fragment from the gel (Experiment 4).
	www.zoo.utoronto.ca /able/volumes/vol-12/1-karche/1-karche.htm (9081 words)

	Bio572: Detection and hybridization
		The nicks in the DNA are "translated," or moved along the backbone, by incorporation of new nucleotides.
		To say it a different way, when hybridizing a probe to the DNA or RNA on a membrane, we adjust the solution conditions (for example, the salt concentration) so that the melting point of the nucleic acids is approximately 20-25 degrees higher than the incubation temperature.
		In general, the DNA on the filter is denatured into single strands before it is blotted, and the probe is boiled (denatured) before it is added to the hybridization mixture.
	escience.ws /b572/L22/L22.htm (2734 words)

	Negative Ion SIMS Detection of DNA Hybridization
		Peptide nucleic acid (PNA) is similar to DNA except the deoxyribose- phosphate backbone in DNA is replaced by polyamide structure.
		In this unique detection method, evidence of hybridization of DNA to PNA is provided by the presence of PO and PO in the negative secondary ion mass spectrum of the probe site.
		However, in this publication, laser-based ionization mass spectrometry was used to detect phosphorus atoms as an indication of DNA hybridization to the PNA probes.
	www.atom-sci.com /DNA-PNA.htm (284 words)

	Electrical Detection of DNA Hybridization
		This conductor- insulator- conductor combination has a characteristic capacitance, which will decrease when the volume of the insulating layer is increased by hybridization of DNA to the probe.
		In addition, we were able to observe a small but sharp rise in capacitance due to dissociation of the hybrid when the hybridization solution was warmed.
		This ability to determine the melting temperature for each hybrid on the array would allow discrimination of single-base mismatches at fixed conditions (it would not be necessary to vary stringency conditions for different sets of probes).
	www.atom-sci.com /capacitance.htm (280 words)

	Bioinquiry: DNA-DNA Hybrid Technique
		DNA-DNA hybridization is a technique used to compare the relationship between two species of organisms.
		this technique uses heat to split two DNA molecules, each from a different species or organism, and allows one strand from one species to combine with a strand (a "complementary" strand) of another species.
		Assume that you are comparing DNA samples from the cheetah, King cheetah, lion and domestic cat.
	bioinquiry.biol.vt.edu /bioinquiry/Cheetah/cheetahpaid/cheetahhtmls/dnahybrid.html (285 words)

	Bio572: Detection and hybridization
		To say it a different way, when hybridizing a probe to the DNA or RNA on a membrane, we adjust the solution conditions (for example, the salt concentration) so that the melting point of the nucleic acids is approximately 20-25 degrees higher than the incubation temperature.
		In general, the DNA on the filter is denatured into single strands before it is blotted, and the probe is boiled (denatured) before it is added to the hybridization mixture.
		If you hope to use the intensity of hybridization to reflect the amount of material in your target band, the total amount of your probe should be in excess over the amount of target DNA on your blot.
	www.escience.ws /b572/L22/L22.htm (2734 words)

	The DNA-DNA Hybridization technique
		The hybrid molecules are then dissociated ("melted") in a thermal gradient under controlled conditions such that a measure of the melting temperature of the hybrid duplex may be calculated.
		The melting temperature of a DNA duplex molecule is a function of the number of correctly base-paired nucleotides, thus it is a measure of the degree of genetic similarity between the two single strands forming the duplex.
		The DNA hybridization comparisons showed that the grebes are indeed distant from other living groups, but the loons cluster with the penguins and tubenoses (petrels, shearwaters, albatrosses).
	www.scricciolo.com /classificazione/sequence7.htm (2793 words)

	Electrophoresis, DNA Markers: DNA Markers for Genomic DNA Analysis
		DNA Marker I for Genomic DNA Analysis is supplied with 10X Loading Dye Solution.
		DNA Marker II for Genomic DNA Analysis is supplied with 10X Loading Dye Solution.
		DNAs are separately digested to completion with the appropriate Fermentas PureExtreme® restriction endonuclease(s), purified, dissolved in a storage buffer and then mixed.
	www.fermentas.com /catalog/electrophoresis/genomicmarkers.htm (573 words)

	[No title]
		The probe should be isolated in the same manner as the DNA construct used for microinjection, with the exception that following gel elution, column purification is not required.
		The probe should not hybridize to normal mouse DNA under conditions of reasonable stringency.
		If Southern blot is required to distinguish endogenous genes (normal C57BL/6, SJL, or FVB mouse DNA) from transgenes, be aware that sensitivity may not be sufficient to identify mosaic founders.
	www.urmc.rochester.edu /research/transgenic/word/dna.doc (153 words)

	DNA Hybridization Analysis
		The two types of DNA are allowed to form double-stranded hybrid molecules and the extent of hybridization is measured using a simple color-producing enzyme reaction.
		The DNA fragment containing the control region is then identified by hybridization analysis using a biotinylated probe for the control region and the enzyme-color-producing assay.
		Following electrophoresis, the DNA in the gel is transferred to a nylon membrane during a 15-minute blotting step and the viral DNA on the blot is then detected by using an enzyme-color-producing reaction.
	www.modernbio.com /dna_hybridization_analysis.htm (1032 words)

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