An oligonucleotide from Greek Language Greek prefix oligo , having few, having little is a short nucleic acid polymer , typically with fifty or fewer nucleotide bases . Although they can be formed by bond cleavage of longer segments, they are now more commonly oligonucleotide synthesis synthesized , in a sequence specific manner, from individual Nucleoside phosphoramidite nucleoside phosphoramidites . Automated synthesizers allow the synthesis of oligonucleotides up to about 200 bases. Oligonucleotides are characterized by the Nucleic acid sequence sequence of nucleotide residues that comprise the entire molecule. The length of the oligonucleotide is usually denoted by Monomer mer from Greek Language Greek meros , part . For example, a fragment of 25 bases would be called a 25 mer. Oligonucleotides readily bind, in a sequence specific manner, to their respective Complementarity molecular biology complementary oligonucleotides, DNA, or RNA to form Nucleic acid thermodynamics Concepts duplexes or, less often, hybrids of a higher order. This basic property serves as a foundation for the use of oligonucleotides as Hybridization probe probes for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarray s, Southern blot s, Allele specific oligonucleotide ASO analysis , fluorescent in situ hybridization FISH , and the synthesis of artificial genes. Oligonucleotides are also indispensable elements in antisense gene therapy. Oligonucleotides composed of Nucleotide 2 deoxyribonucleotides oligodeoxyribonucleotides are fragments of DNA and are often used ... of DNA. There, the oligonucleotide is referred to as a Primer molecular biology primer , allowing DNA polymerase to extend the oligonucleotide and replicate the complementary strand. Synthesis Main oligonucleotide ... compounds. The oligonucleotide chain assembly proceeds in the direction from 3 to 5 terminus ... gl Oligonucle tido id Oligonukleotida it Oligonucleotide lt Oligonukleotidas ja ... more details
Oligonucleotide synthesis is the chemical synthesis of relatively short fragments of nucleic acid s with defined ... oligonucleotide synthesis is carried out in the opposite, 3 to 5 direction. Currently, the process ... the desired oligonucleotide, the building blocks are sequentially coupled to the growing oligonucleotide ... to about 200 nucleotide residues because the number of errors accumulates with the length of the oligonucleotide ... s. History The evolution of oligonucleotide synthesis saw four major methods of the formation of internucleosidic ..., Baron Todd Alexander Todd s group pioneered H phosphonate and phosphate triester methods of oligonucleotide ... Scheme. 2. Synthetic cycle in H phosphonate method of oligonucleotide synthesis. X O, S Thirty years ... X S . Phosphodiester synthesis File phosphodiester method.png thumb 300px Scheme. 3 Oligonucleotide ... brown Phosphotriester synthesis File phosphotriester method.png thumb 300px Scheme 4. Oligonucleotide ... led to the automation of the oligonucleotide chain assembly. Phosphite triester synthesis ... Protecting group Me methyl group led to the nucleoside phosphoramidites currently used in oligonucleotide ... of the oligonucleotide chain assembly, all the protecting groups are removed to yield the desired ... soluble in acetonitrile , the solvent commonly used in oligonucleotide synthesis. In contrast ... steps in the synthetic cycle, the oligonucleotide chain assembly may be carried out using dA and dC ... protected over the entire length of the oligonucleotide chain assembly. The protection of the exocyclic .... ref name sinha Once a phosphoramidite has been coupled to the solid support bound oligonucleotide ... bound oligonucleotide see Step 2 Coupling below . Non nucleoside phosphoramidites File Nonnucleoside ... of oligonucleotides by phosphoramidite method. Oligonucleotide synthesis is carried out ... support bound oligonucleotide precursor bearing a free 5 terminal hydroxyl group. It is worth ... of acids leads to depurination of solid support bound oligonucleotide and thus reduces the yield ... more details
Orphan date November 2006 Methylation specific oligonucleotide microarray was developed as a technique to map methylation changes in DNA in cancer . This technique was developed by Professor Tim Hui Ming Huang and was published in journal Genome Research on 2002 Gitan et al., 2002 . The method utilizes bisulfite modified DNA that is used as templates for PCR amplification , which is subsequently hybridized to oligonucleotide microarray. External links Commons Methylation specific oligonucleotide microarray http www.epigeneticstation.com Resources, information and specific protocols for DNA Methylation Analysis Category Cancer research Category Microarrays genetics stub medicine stub ... more details
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 Hybridization probe probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay. It is a common tool used in genetic testing , forensics , and Molecular Biology research. An ASO is typically an oligonucleotide of 15 21 nucleotide nucleotide bases in length. It is designed and used in a way that makes it specific for only one version, or allele , of the DNA being tested. The length of the ASO, which strand it is chosen from, and the conditions by which it is Nucleic acid hybridization bound to and washed from the target DNA all play a role in its specificity. These probes can usually be designed to detect a difference of as little as 1 base in the target s genetic sequence, a basic ability in the assay of single nucleotide polymorphism s SNPs , important in genotype genotype analysis and the Human Genome Project . To be detected after it has bound to its target, the ASO must be labeled with a radioactive, enzymatic, or fluorescent tag. The Illumina Methylation Assay technology takes advantage of ASO to detect one base pair difference cytosine versus thymine to measure methylation at a specific CpG site. Example image ASODemo.jpg right thumb 350px center Binding of the S ASO probe to S DNA top or A DNA bottom . center The human disease sickle cell disease sickle cell anemia is caused by a genetic mutation in the codon for the sixth amino acid of the blood protein HBB beta hemoglobin . The normal ... RB Discrimination among the human beta A, beta S, and beta C globin genes using allele specific oligonucleotide ... Enzyme . The RFLP assay was briefly adapted to the use of oligonucleotide Oligomer restriction ... globin and HLA DQ DNA with allele specific oligonucleotide probes Nature vol. 324 6093 pp. 163 166 ... biology scarr ASO test for CF2.html Image of ASO autoradiogram DEFAULTSORT Allele Specific Oligonucleotide ... more details
Notability date December 2009 Short Oligonucleotide Analysis Package SOAP is a bioinformatics package used for the assembly and analysis of DNA sequences. SOAP is particularly well suited for Illumina company Illumina next generation sequences. There are 5 members in this package SOAPaligner A new alignment tool from SOAP v1. SOAPdenovo A short reads do novo assembler. SOAPsnp An accurate consensus sequence builder. SOAPsv A structural variation scanner. SOAPindel A tool to find insertion and deletion specially for re sequence technology. All programs in the SOAP package may be used free of charge. SOAPdenovo, a program in the SOAP package, was used to assemble the Panda genome entirely from short Illumina next generation sequences http www.nature.com nature journal v463 n7279 full nature08696.html . SOAP v1 SOAP v1 is the previous version of SOAPaligner, and it is only a sequence alignment tool while SOAP SOAP v2 is a program package that contains 5 members as above . See also genomics genome sequencing genome assembly bioinformatics External links http soap.genomics.org.cn http soap.genomics.org.cn soap1 http bioinformatics.genomics.org.cn http seqanswers.com forums showthread.php?t 43 References http bioinformatics.oxfordjournals.org cgi content abstract btp336 SOAP2 an improved ultrafast tool for short read alignment http www.nature.com nature journal v463 n7279 full nature08696.html The sequence and de novo assembly of the giant panda genome Category Bioinformatics Category Bioinformatics software ... more details
Expert subject Genetics date February 2009 Image ROMA.jpg right 270px thumb ROMA. Representational oligonucleotide microarray analysis ROMA is a technique that was developed by Michael Wigler and Rob Lucito at the Cold Spring Harbor Laboratory CSHL in 2003. Fact date July 2008 Wigler and Lucito currently run laboratories at CSHL using ROMA to explore genomic copy number variation in cancer and other genetic diseases. In this technique, two genome s are compared for their differences in copy number on a microarray. The ROMA technology emerged from a previous method called Representational Difference Analysis RDA . ROMA, in comparison to other comparative genomic hybridization CGH techniques, has the advantage of reducing the complexity of a genome with a restriction enzyme which highly increases the efficiency of genomic fragment hybridization to a microarray. In ROMA, a genome is digested with a restriction enzyme, ligated with adapters specific to the restriction fragment sticky ends and amplified by PCR. After the PCR step, representations of the entire genome restriction fragments are amplified to pronounce relative increases, decreases or preserve equal copy number in the two genomes. The representations of the two different genomes are labeled with different fluorophores and co hybridized to a microarray with probes specific to locations across the entire human genome. After analysis of the ROMA microarray image is completed, a copy number profile of the entire human genome is generated. This allows researchers to detect with high accuracy amplifications amplicons and deletions that occur across the entire genome. In cancer, the genome becomes very unstable, resulting in specific regions that may be deleted if they contain a tumor suppressor or amplified if they contain an oncogene . Amplifications and deletions have also been observed in the normal human population ..., R. et al. 2003 Representational oligonucleotide microarray analysis a high resolution method to detect ... more details
unreferenced date December 2010 The genomic signature refers to the characteristic frequency of oligonucleotide s in a genome or sequence. It has been observed that the genomic signature of phylogenetically related genomes is similar. DEFAULTSORT Genomic Signature Category Nucleic acids ... more details
dabconcept DNA synthesis commonly refers to DNA replication DNA biosynthesis in vivo DNA amplification Polymerase chain reaction enzymatic DNA synthesis in vitro DNA amplification Oligonucleotide synthesis chemical synthesis of nucleic acids Gene synthesis physically creating artificial gene sequences disamb ... more details
Oligo may refer to Oligonucleotide as an abbreviation. OLIGO Primer Analysis Software disambiguation Short pages monitor This long comment was added to the page to prevent it being listed on Special Shortpages. It and the accompanying monitoring template were generated via Template Longcomment. Please do not remove the monitor template without removing the comment as well. ... more details
Fluorescein amidite , File FAM Amidite.png thumb 300px Non nucleoside phosphoramidites for 5 modification of synthetic oligonucleotides abbreviated as FAM commercially available 6 FAM version ref Brush, C. K. Fluorescein Labelled Phosphoramidites. US Patent 5,583,236. http patft.uspto.gov netacgi nph Parser?Sect1 PTO2&Sect2 HITOFF&p 1&u 2Fnetahtml 2FPTO 2Fsearch bool.html&r 15&f G&l 50&co1 AND&d PTXT&s1 5,583,236&OS 5,583,236&RS 5,583,236 ref is shown in Figure , is an important synthetic equivalent of fluorescein dye used in oligonucleotide synthesis and molecular biology . FAM is used in the preparation of fluorescein labeled oligonucleotide probes for the detection of the presence of the complementary nucleic acid s or primers for polymerase chain reaction . Oligonucleotides labeled with fluorescein at one of the termini and with a Quenching fluorescence quencher at the other can serve as molecular beacon s. Category Fluorone dyes Reflist ... more details
The nucleotide universal IDentifier nuID is designed to uniquely and globally identify oligonucleotide microarray probes. br Oligonucleotide probes of microarrays that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company s microarray and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis identification of the genes hybridizing to that probe. This also makes data interpretation and integration of different batches of data difficult. nuID was designed to solve these problems. It is a unique, non Degeneracy degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. The designed of nuID was inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non degenerately transforms the sequence itself into a compact identifier a lossless compression . In addition, a redundancy check checksum was added to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, encryption schema can also be added for nuID. The utility of nuIDs has been implemented for the annotation of Illumina company Illumina microarrays, which can be downloaded from Bioconductor website http www.bioconductor.org . It also has universal applicability as a source independent naming convention for oligomers. The nuID schema has three significant advantages over using the oligo sequence directly as an identifier first it is more compact due to the base 64 encoding second, it has a built in error detection and self identification and third, it can be encrypted in cases ... more details
Single base extension SBE is a method for determining the identity of a nucleotide base at a specific position along a nucleic acid . The method is used to identify a single nucleotide polymorphism SNP . In the method, an oligonucleotide primer hybridizes to a complementary region along the nucleic acid, to form a duplex, with the primer s terminal 3 end directly adjacent to the nucleotide base to be identified. The oligonucleotide primer is enzymatically extended a single base by a nucleotide terminator complementary to the nucleotide being identified. The terminator prevents additional nucleotides from being incorporated. Many approaches can be taken for determining the identity of a terminator, including fluorescence labeling, mass labeling for mass spectrometry, measuring enzyme activity using a protein moiety, and isotope labeling. The method was invented by Phillip Goelet, Michael Knapp and Stephen Anderson while working at the company Molecular Tool. The Illumina Methylation Assay utilizes this method in their Infinium technology to measure DNA methylation levels in the human genome. References Philip Goelet, Michael R. Knapp, Stephen Anderson, 1999 , U.S. Patent No 5,888,819. Washington, DC U.S. Patent and Trademark Office. Category Genetics de Single Base Extension ... more details
Infobox rfam Name C0465 RNA image RF00116.jpg width caption Predicted secondary structure and sequence conservation of C0465 Symbol C0465 AltSymbols Rfam RF00116 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0465 RNA is a bacterial non coding RNA of 78 nucleotides in length that is found between the tar and cheW gene s in the genomes of Escherichia coli and Shigella flexneri . This ncRNA was originally identified in E.coli using microarray high density oligonucleotide probe arrays microarray ref name pmid12202758 cite journal author Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res. volume 30 issue 17 pages 3732 8 year 2002 pmid 12202758 doi 10.1093 nar gkf505 pmc 137427 ref . The function of this ncRNA is unknown. See also C0299 RNA C0343 RNA C0719 RNA References references External links Rfam id RF00116 name C0465 RNA DEFAULTSORT C0465 Rna Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name C0719 RNA image RF00117.jpg width caption Predicted secondary structure and sequence conservation of C0719 Symbol C0719 AltSymbols Rfam RF00117 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0719 RNA is a bacterial non coding RNA of 222 nucleotides in length that is found between the yghK and glcB gene s in the genomes of Escherichia coli and Shigella flexneri . This non coding RNA was originally identified in E.coli using microarray high density oligonucleotide probe arrays microarray. ref name pmid12202758 cite journal author Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res. volume 30 issue 17 pages 3732 8 year 2002 pmid 12202758 doi 10.1093 nar gkf505 pmc 137427 ref The function of this ncRNA is unknown. See also C0299 RNA C0343 RNA C0465 RNA References references External links Rfam id RF00117 name C0719 RNA DEFAULTSORT C0719 Rna Category Non coding RNA molecular cell biology stub ... more details
Orphan date May 2011 LY2181308 is an antisense oligonucleotide that complementarily binds to survivin mRNA and inhibits its expression in tumor tissue. ref cite journal pmid 21079959 title Phase I study of LY2181308, an antisense oligonucleotide against survivin, in patients with advanced solid tumors. date Nov 2010 ref It being investigated for a number of different cancers. ref http clinicaltrials.gov ct2 results?term LY2181308 ref It is targeted at survivin which prevents cells dying. ref http www.isispharm.com Pipeline Therapeutic Areas Cancer.htm LY2181308 ref Clinical trials It has completed a phase II trial for acute myeloid leukemia . ref http clinicaltrials.gov ct2 show NCT00620321 A phase II Study of LY2181308 Sodium in Patients With Relapsed or Refractory Acute Myeloid Leukemia ref A phase II trial for non small cell lung cancer has started. ref http clinicaltrials.gov ct2 show NCT01107444 A Phase II Study of LY2181308 in Combination With Docetaxel Versus Docetaxel in Patients With Non Small Cell Lung Cancer ref A phase II trial for hormone refractory prostate cancer will run until early 2012. ref http clinicaltrials.gov ct2 show NCT00642018 A Phase II Study of an Experimental Chemotherapy Combination to Treat Hormone Refractory Prostate Cancer ref References reflist Category Nucleic acids antineoplastic drug stub ... more details
sisterlinks q no commons no species no s no n no A microarray is a multiplex assay multiplex lab on a chip . It is a 2D array on a Substrate materials science solid substrate usually a glass slide or silicon thin film cell that assays large amounts of biological material using high throughput screening methods. Types of microarrays include DNA microarray s, such as cDNA microarrays, oligonucleotide microarrays and SNP microarrays MMChip s, for surveillance of microRNA populations Protein microarray s Peptide microarray s, for detailed analyses or optimization of protein protein interactions Tissue microarray s Cellular microarray s also called transfection microarrays Chemical compound microarray s Antibody microarray s Carbohydrate array s glycoarrays Category Microarrays de Microarray nl microarray ja ur ... more details
Avecia was a privately owned group of biotechnology companies with recognised leading positions in process development and manufacture of biological and oligonucleotide pharmaceuticals, and had their international headquarters in Blackley , Manchester , United Kingdom . The group s Biologics business, based in Billingham UK, was acquired first by Merck and then subsequently became Fujifilm Diosynth Biotechnologies in April 2011. The group s OligoMedicines business was acquired by Nitto Denko in February 2011, and so the Avecia Group no longer exists as a trading company. External links http www.avecia.com Avecia.com Category Chemical companies of the United Kingdom Category Companies based in Manchester chemical company stub ... more details
acid sequence is present in the test sample. Synthesis main Oligonucleotide synthesis Molecular beacons are oligonucleotide synthesis synthetic oligonucleotide s whose preparation is well documented ... more details
Unreferenced stub auto yes date December 2009 S1 nuclease is an endonuclease that is active against single stranded DNA and RNA molecules. It is five times more active on DNA than RNA. Its reaction products are oligonucleotide s or single nucleotide s with 5 phosphorylation phosphoryl groups. Although its primary substrate is single stranded, it can also occasionally introduce single stranded breaks in double stranded DNA or RNA, or DNA RNA hybrids. It is used in the laboratory as a reagent in nuclease protection assay s. In molecular biology, it is used in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA. DEFAULTSORT S1 Nuclease Category Enzymes Enzyme stub ... more details
Multiple issues cleanup August 2009 orphan August 2009 Restriction Fragment Mass Polymorphism RFMP is a technology which Restriction digest digests DNA into oligonucleotide fragments, and detects variation of DNA sequence s by molecular weight of the fragments. RFMP is a Property proprietary technology of GeneMatrix and can be utilized for genotyping viruses and microorganisms , and for human genome research. References Kim, Y 2005 . Population Genotyping of Hepatitis C Virus by Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry Analysis of Short DNA Fragments , Clinical Chemistry , 51 1123 1131 External links http www.genematrix.net eng sic 01.htm RFMP platform technology Category DNA sequencing biotech stub ... more details
A random hexamer or random hexonucleotides are for various polymerase chain reaction PCR applications such as rolling circle amplification to prime the DNA. They are oligonucleotide sequences of 6 bases which are synthesised entirely randomly to give a numerous range of sequences that have the potential to anneal at many random points on a DNA sequence and act as a primer to commence first strand cDNA synthesis. ref http www.invitrogen.com site us en home References protocols nucleic acid amplification and expression profiling pcr protocol pcr and rt pcr.html ref References reflist http www.fermentas.com en products all nucleotides primers other primers so142 random hexamer primer Category Polymerase chain reaction ... more details
merge site directed mutagenesis discuss Talk PCR mutagenesis Merger proposal date August 2010 Multiple issues unreferenced January 2010 context January 2010 PCR mutagenesis is a method for generating site directed mutagenesis . This method can generate mutations base substitutions, insertions, and deletions without the need for subcloning into M13 based bacteriophage vectors and for ssDNA rescue. The procedure involves a PCR reaction using a plasmid or chromosomal DNA as template and synthetic oligonucleotide primers containing the desired mutation with each complementary to the opposite strands of the vector. DEFAULTSORT Pcr Mutagenesis Category Mutagenesis genetics stub ... more details
REG1 is an anticoagulation system. It involves inhibition of Factor IX a. ref name pmid20072947 cite journal author Becker RC, Chan MY title REG 1, a regimen comprising RB 006, a Factor IXa antagonist, and its oligonucleotide active control agent RB 007 for the potential treatment of arterial thrombosis journal Curr. Opin. Mol. Ther. volume 11 issue 6 pages 707 15 year 2009 month December pmid 20072947 doi url ref References reflist biology stub Category Anticoagulants Category Human proteins ... more details
multiple issues context November 2011 one source November 2011 wikify November 2011 ChIRP Seq is a high throughput sequencing method to discover RNA bound DNA and proteins. The RNA sequences of interest are hybridized to oligonucleotide tiles using biotin streptavidin . The chromatin fraction that is bound to the beads is then determined using high throughput sequencing . ref cite journal last Chu first Ci coauthors Qu, Kun, Zhong, Franklin L., Artandi, Steven E., Chang, Howard Y. title Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA Chromatin Interactions journal Molecular Cell date 31 August 2011 doi 10.1016 j.molcel.2011.08.027 ref References Reflist Category DNA sequencing biochem stub ... more details
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