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*  DECIPHER (software)
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 ...
*  Biotechnology in pharmaceutical manufacturing
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 ...
*  T44 RNA
"Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays". Nucleic Acids Res. 30 (17): 3732- ...
*  Gene expression
... 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 ...
*  Chimera (EST)
"EST Assembly for the Creation of Oligonucleotide Probe Targets" (PDF). Agilent Technologies. Retrieved May 12, 2009. Maidak, B ...
*  HLA-DPB1
"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 ...
*  HLA-A33
Williams F, Meenagh A, Maxwell AP, Middleton D (1999). "Allele resolution of HLA-A using oligonucleotide probes in a two-stage ...
*  C0719 RNA
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 ...
*  Fluorescence in situ hybridization
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 ...
*  DNA-functionalized quantum dots
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 ...
*  Restriction fragment length polymorphism
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 ...
*  Proximity ligation assay
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 ...
*  History of polymerase chain reaction
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 ...
*  HLA-DRB3 (gene)
"High-resolution analysis of the human HLA-DR polymorphism by hybridization with sequence-specific oligonucleotide probes". Proc ...
*  Transcriptomics technologies
The mRNA molecules can be separated using oligonucleotides probes which bind their poly-A tails. Alternatively, ribo-depletion ... The fluorescence intensity at each probe location on the array indicates the transcript abundance for that probe sequence. ... The probes are longer than those of high-density arrays and typically lack the transcript resolution of high-density arrays. ... Both spotted oligonucleotide arrays and Affymetrix high-density arrays were the method of choice for transcriptional profiling ...
*  SNP genotyping
In the oligonucleotide ligase assay, two probes are designed; an allele-specific probe which hybridizes to the target DNA so ... The first probe, called the Invader oligonucleotide is complementary to the 3' end of the target DNA. The last base of the ... In high-density oligonucleotide SNP arrays, hundreds of thousands of probes are arrayed on a small chip, allowing for many SNPs ... The oligonucleotide is designed such that there are complementary regions at each end and a probe sequence located in between. ...
*  Syntrophomonas curvata
"Quantification of syntrophic fatty acid-β-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe ...
*  MtDNA control region
... of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes". Am. ...
*  Degradomics
Traditionally DNA microarrays use complementary DNA or oligonucleotide probes to analyze messenger RNA (mRNA) from genes of ... Two techniques are activity-based probes (ABPs) and Proteolytic Signature Peptides (PSPs). ABP molecules serve as probes to ... For proteases, specific probes for protease genes and their inhibitors have been developed to view expression patterns on the ... U.S.A., 99 (17) 11139-11144 (2002). Saghatelian A., Jessani N., Joseph A., Humphrey M., Cravatt B.F. Activity-based probes for ...
*  Oligomer 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 ...
*  Sequencing by ligation
The oligonucleotide probes may also be constructed with cleavable linkages which can be cleaved after identifying the label. ... A mixed pool of probe oligonucleotides is then brought in (eight or nine bases long), labeled (typically with fluorescent dyes ... depending on which end of the probe oligonucleotides are blocked by the label. The 3'-5' direction is more efficient for doing ... This will both remove the label and regenerate a 5' phosphate on the end of the ligated probe, preparing the system for another ...
*  ChiRP-Seq
Overview of ChiRP-Seq method: Tens of oligonucleotide probes are designed to be complementary to the RNA of interest. These ... These chromatin fragments were hybridized to the biotinylated probe set. Complexes containing biotin-probe + RNA of interest + ...
*  Molecular Inversion Probe
Here, traditional, linear oligonucleotide probes failed to yield results. Thus, padlock probes possess sufficient specificity ... If array-based approach is used, the probe may optionally contain a probe-specific tag that uniquely identifies the probe as ... similar to the probe-release site, is also a restriction site. Anneal probe to genomic target DNA Probes are added to the ... resulting in a fully circularized probe. Remove non-reacted probes Since gap filling is not performed for non-reacted probes, ...
*  Massive parallel sequencing
The surface of the beads contains oligonucleotide probes with sequences that are complementary to the adaptors binding the DNA ... Non-ligated probes are washed away, followed by fluorescence imaging to determine the identity of the ligated probe. The cycle ... In its simplest form, a fluorescently labelled probe hybridizes to its complementary sequence adjacent to the primed template. ... is not carried out by polymerases but rather by DNA ligase and either one-base-encoded probes or two-base-encoded probes. ...
*  Wood turtle
DNA fingerprinting of turtles involves using an oligonucleotide probe to produce gender specific markers, ultimately providing ...
*  Multiplex ligation-dependent probe amplification
Each probe consists of two oligonucleotides which recognize adjacent target sites on the DNA. One probe oligonucleotide ... Only when both probe oligonucleotides are hybridized to their respective targets, can they be ligated into a complete probe. ... The advantage of splitting the probe into two parts is that only the ligated oligonucleotides, but not the unbound probe ... If the probes were not split in this way, the primer sequences at either end would cause the probes to be amplified regardless ...