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Webtag: a new web tool providing tags/anchors for RT-PCR experiments with prokaryotes.

Pinto FL, Svensson H, Lindblad P - BMC Biotechnol. (2007)

Bottom Line: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome.These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Photochemistry and Molecular Science, The Angström Laboratories, Uppsala University, Box 523, SE-75120, Uppsala, Sweden. fernando.lopespinto@fotomol.uu.se

ABSTRACT

Background: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome. These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.

Results: The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

Conclusion: This new web tool allows scientists to easily and rapidly obtain suitable tags for RT-PCR experiments, and is available at http://www.egs.uu.se/software/webtag/.

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Related in: MedlinePlus

Schematic illustrating the advantages associated with the use of tags/anchors to circumvent gDNA contamination. During reverse transcriptase (A) the tag/anchor is included the cDNA allowing its specific amplification during PCR (B).
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Figure 1: Schematic illustrating the advantages associated with the use of tags/anchors to circumvent gDNA contamination. During reverse transcriptase (A) the tag/anchor is included the cDNA allowing its specific amplification during PCR (B).

Mentions: One proposed strategy leading to the specific amplification of cDNA involves the use of anchors/tags [4,9,12]. As illustrated in Figure 1, during reverse transcription of mRNA, a unique tag positioned at the 5'end of the gene specific primer is included in the cDNA. This tag will later be used as primer targeting the second cDNA strand. Application of this strategy, like in the cases of RS-PCR [4] and (EXACT) RT-PCR [9], results in RNA-specific amplification without loss of sensitivity.


Webtag: a new web tool providing tags/anchors for RT-PCR experiments with prokaryotes.

Pinto FL, Svensson H, Lindblad P - BMC Biotechnol. (2007)

Schematic illustrating the advantages associated with the use of tags/anchors to circumvent gDNA contamination. During reverse transcriptase (A) the tag/anchor is included the cDNA allowing its specific amplification during PCR (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2147000&req=5

Figure 1: Schematic illustrating the advantages associated with the use of tags/anchors to circumvent gDNA contamination. During reverse transcriptase (A) the tag/anchor is included the cDNA allowing its specific amplification during PCR (B).
Mentions: One proposed strategy leading to the specific amplification of cDNA involves the use of anchors/tags [4,9,12]. As illustrated in Figure 1, during reverse transcription of mRNA, a unique tag positioned at the 5'end of the gene specific primer is included in the cDNA. This tag will later be used as primer targeting the second cDNA strand. Application of this strategy, like in the cases of RS-PCR [4] and (EXACT) RT-PCR [9], results in RNA-specific amplification without loss of sensitivity.

Bottom Line: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome.These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Photochemistry and Molecular Science, The Angström Laboratories, Uppsala University, Box 523, SE-75120, Uppsala, Sweden. fernando.lopespinto@fotomol.uu.se

ABSTRACT

Background: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome. These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination.

Results: The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures.

Conclusion: This new web tool allows scientists to easily and rapidly obtain suitable tags for RT-PCR experiments, and is available at http://www.egs.uu.se/software/webtag/.

Show MeSH
Related in: MedlinePlus