Oligonucleotide design: primer design for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization ... Noguera DR, Wright ES, Camejo P, Yilmaz LS (2014). "Mathematical tools to optimize the design of oligonucleotide probes and ... "Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for ... "Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics". PLOS ...
A unique oligonucleotide... homologous to Factor IX mRNA... was synthesized and labeled... The resultant probe was used to ... yielded sufficient amino acid sequence to construct oligonucleotide probes. The known sequence of Factor IX RNA was then used ... with a Factor IX cDNA probe. Hybridizing recombinant phage were isolated, plaque-purified, and the DNA isolated. Restriction ...
"Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732- ...
... s are oligonucleotide hybridization probes that can report the presence of specific nucleic acids in homogenous ... 5'-nuclease TaqMan assay Exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes. SNP detection ... They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess ... The term more often used is molecular beacon probes. Molecular beacons are hairpin shaped molecules with an internally quenched ...
... fluorescently labeled oligonucleotide probes are more expensive than non-specific intercalating fluorescent dyes. For ... The probed sample is then observed by microscopy to identify where the mRNA or protein is. By replacing the gene with a new ... A single array or "chip" may contain probes to determine transcript levels for every known gene in the genome of one or more ... A sample of RNA is separated on an agarose gel and hybridized to a radioactively labeled RNA probe that is complementary to the ...
"EST Assembly for the Creation of Oligonucleotide Probe Targets" (PDF). Agilent Technologies. Retrieved May 12, 2009. Maidak, B ...
"Rapid HLA-DPB typing using enzymatically amplified DNA and nonradioactive sequence-specific oligonucleotide probes". ... 1991). "Positive correlation between oligonucleotide typing and T-cell recognition of HLA-DP molecules". Immunogenetics. 34 (1 ...
Williams F, Meenagh A, Maxwell AP, Middleton D (1999). "Allele resolution of HLA-A using oligonucleotide probes in a two-stage ...
Blencowe BJ, Sproat BS, Ryder U, Barabino S, Lamond AI (November 1989). "Antisense probing of the human U4/U6 snRNP with ... biotinylated 2'-OMe RNA oligonucleotides". Cell. 59 (3): 531-9. doi:10.1016/0092-8674(89)90036-6. PMID 2478298. Raghunathan PL ... Mougin A, Gottschalk A, Fabrizio P, Lührmann R, Branlant C (April 2002). "Direct probing of RNA structure and RNA-protein ... Several experiments involving X-ray crystallography, NMR, and chemical modification RNA structure probing indicate that U4 ...
This non-coding RNA was originally identified in E.coli using high-density oligonucleotide probe arrays (microarray.) The ... "Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732-8 ...
... this type of probe is known as an allele-specific oligonucleotide. One of the bead types will correspond to the methylated ... Both bead types are attached to single-stranded 50-mer DNA oligonucleotides that differ in sequence only at the free end; ... This assay is used for methylation probes on the Illumina Infinium HumanMethylation27 BeadChip (henceforth, 27k [methylation] ... and hybridized to the chip via allele-specific annealing to either the methylation-specific probe or the non-methylation probe ...
Each probe for the detection of mRNA and lncRNA is composed of 20 oligonucleotide pairs, each pair covering a space of 40-50 bp ... Probe size is important because longer probes hybridize less specifically than shorter probes, so that short strands of DNA or ... The mixture of probe sequences determines the type of feature the probe can detect. Probes that hybridize along an entire ... A target-specific probe, composed of 20 oligonucleotide pairs, hybridizes to the target RNA(s). Separate but compatible signal ...
Amine-modified oligonucleotide probes attached to carboxyl groups on quantum dots show sequence-specific hybridization. These ... The increased solubility is necessary in order to allow quantum dots to be used as a DNA imaging probe in a biological system. ... Pinaud, Fabien; Clarke, Samuel; Sittner, Assa; Dahan, Maxime (30 March 2010). "Probing cellular events, one quantum dot at a ... probes can also detect low expressing genes. This potentially allows researchers to understand when and where certain proteins ...
In this methods, one or both strands of encoding genes can be used as probes. In addition to computational searches and ... Although neurons and glia have been shown to have the ability to freely uptake naked antisense oligonucleotides, a traceable ... Fomivirsen, a 21 base-pair oligonucleotide, was developed to treat cytomegalovirus retinitis in patients with AIDS. It works by ... The most common chemical modification on the oligonucleotides is adding a phophorothioate linkage to the backbones. However, ...
A limited version of the RFLP method that used oligonucleotide probes was reported in 1985. Fortunately, the results of the ... the amplified segment can be analyzed by Allele specific oligonucleotide (ASO) probes, a process that can often be done by a ... In the first schematic, a small segment of the genome is being detected by a DNA probe (thicker line). In allele "A", the ... In allele "d" there are only two repeats in the VNTR, so the probe detects a shorter fragment between the same two restriction ...
A labeled oligonucleotide probe is hybridized to a target DNA, and then treated with a restriction enzyme. If the probe exactly ... In part 1a of the schematic the oligonucleotide probe, labeled on its left end (asterisk), is shown on the top line. It is ... It is difficult to label oligonucleotides to a level high enough to use them as probes for genomic DNA. This problem also ... It is difficult to design oligonucleotides and use them in a way that they become hybridization probes for just a single site ...
Next, fluorescent-labeled complementary oligonucleotide probes are added, and they bind to the amplified DNA. The resulting ... Each of the PLA probes has a unique short DNA strand attached to it, If the PLA probes are in close proximity (that is, if the ... Secondary antibodies (2o Ab) directed against the constant regions of the different primary antibodies, called PLA probes, bind ...
Oligonucleotide microarrays are designed using pairs of oligonucleotide hybridization probes targeting CpG sites of interest. ... The probes are also bisulfite-specific to prevent binding to DNA incompletely converted by bisulfite. The Illumina Methylation ... Methylated-specific primers are used, and a methylated-specific fluorescence reporter probe is also used that anneals to the ... In alternative fashion, the primers or probe can be designed without methylation specificity if discrimination is needed ...
... is designed to uniquely and globally identify oligonucleotide microarray probes. Oligonucleotide probes of microarrays that are ... of nuID was inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, ... It is a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide ... resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe. This also makes data ...
Instead of probing for sequences of known or predicted genes that may be dispersed throughout the genome, tiling arrays probe ... Another study with Arabidopsis used high-density oligonucleotide arrays that cover the entire genome. More than 10 times more ... Overlapping probes or probes in very close proximity can be used. This gives an unbiased analysis with high resolution. Besides ... or the amount of known base pairs between probe sequences, as well as probe length. For smaller genomes such as Arabidopsis, ...
... and summaries of high density oligonucleotide array probe level data". Biostatistics. 4 (2): 249-64. doi:10.1093/biostatistics/ ... Raw Affy data contains about twenty probes for the same RNA target. Half of these are "mismatch spots", which do not precisely ... The simplest one is to call "significant" any probe that differs by an average of at least twofold between treatment groups. ... The current Affymetrix MAS5 algorithm, which uses both perfect match and mismatch probes, continues to enjoy popularity and do ...
By May 1983 Mullis synthesized oligonucleotide probes for a project at Cetus to analyze a sickle cell anemia mutation. Hearing ... "Analysis of enzymatically amplified β-globin and HLA DQα DNA with allele-specific oligonucleotide probes." Nature vol. 324 ( ... Primers and probes were designed for a variable segment of the Human leukocyte antigen DQα gene. This reaction was much more ... Sequence-specific oligonucleotides were used both as building blocks for the gene, and as primers and templates for DNA ...
"High-resolution analysis of the human HLA-DR polymorphism by hybridization with sequence-specific oligonucleotide probes". Proc ...
... -labelled probes can be imaged using FISH, or targeted by antibodies using immunohistochemistry. The latter is a ... The use of fluorescein amidite shown above allows one to synthesize labeled oligonucleotides for the same purpose. Yet another ... In oligonucleotide synthesis, several phosphoramidite reagents containing protected fluorescein, e.g. 6-FAM phosphoramidite 2, ... Fluorescein can also be conjugated to nucleoside triphosphates and incorporated into a probe enzymatically for in situ ...
A selector consists of two oligonucleotides, one Vector oligonucleotide and one Selector probe. Together they form one Selector ... A selector probe hybridizes with both ends of the selected target. A selector probe hybridizes with one end to the 3' end of ...
It has been especially useful in probing the structure of natural RNA oligonucleotides, which tend to adopt complex ... Two dimensional NMR studies began to be reported in 1982[13] and then, with the advent of oligonucleotide synthesis and more ... NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs. This can be ... Interactions between RNA and metal ions can be probed by a number of methods, including observing changes in chemical shift ...