Webtag is an on-line

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...

tool providing

oligonucleotide Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids ...

sequences In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is called ...

(usually called tags or anchors) that are absent from a specified

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

. These tags can be appended to

gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

specific primers for reverse transcriptase polymerase chain reaction (

RT-PCR Reverse transcription polymerase chain reaction (RT-PCR) is a laboratory technique combining reverse transcription of RNA into DNA (in this context called complementary DNA or cDNA) and amplification of specific DNA targets using polymerase chai ...

) experiments, circumventing genomic DNA contamination.

Background

RT-PCR is a technique used for the detection of even very low copy

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...

transcripts. The sensitivity of the technique also makes it susceptible to DNA contamination. Since

PCR PCR or pcr may refer to: Science * Phosphocreatine, a phosphorylated creatine molecule * Principal component regression, a statistical technique Medicine * Polymerase chain reaction ** COVID-19 testing, often performed using the polymerase chain r ...

is unable to distinguish between

cDNA In genetics, complementary DNA (cDNA) is DNA synthesized from a single-stranded RNA (e.g., messenger RNA (mRNA) or microRNA (miRNA)) template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to express a speci ...

targets and genomic DNA contamination, false positives and/or erroneous quantitative results are possible. In order to overcome genomic DNA contamination in transcriptional studies, reverse template-specific polymerase chain reaction, a modification of RT-PCR is used. The possibility of using tags whose sequences are not found in the genome further improves reverse specific polymerase chain reaction experiments. The use of anchors, or tags, in the 5' region of a gene specific primer or poly-T tail allows for RNA-specific amplification, and constitutes a viable strategy. Techniques such as RS-PCR and (EXACT) RT-PCR are based on the integration of such tags (unique sequences not present in genomic DNA) in the 5' end of the first strand cDNA, permitting RNA-specific amplification without loss of sensitivity.

Webtag

This web based service builds on the Tagenerator tool, but is very fast because all tags are pre-generated and stored in a database. It is also a significant improvement since Webtag takes into account the interactions of the tag with the primers to be used in the experiment. Having it as a web based service also means that the molecular biologist doesn't have to download and install software with all the dependencies on their own computer. Webtag generates tags that combine genome absence with good priming properties for RT-PCR based experiments. The use of such tags will deliberately not result in PCR amplification of genomic DNA, permitting the exclusive amplification of cDNA, therefore circumventing the effects of genomic DNA contamination in an RNA sample.

References

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External links

Official webpage

Tagenerator
Bioinformatics Bioinformatics software