Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic...

Full description

Bibliographic Details
Main Authors:	Kimura, Yasumasa, Soma, Takahiro, Kasahara, Naoko, Delobel, Diane, Hanami, Takeshi, Tanaka, Yuki, de Hoon, Michiel J. L., Hayashizaki, Yoshihide, Usui, Kengo, Harbers, Matthias
Format:	Online
Language:	English
Published:	Public Library of Science 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749234/

id	pubmed-4749234
recordtype	oai_dc
spelling	pubmed-47492342016-02-26 Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays Kimura, Yasumasa Soma, Takahiro Kasahara, Naoko Delobel, Diane Hanami, Takeshi Tanaka, Yuki de Hoon, Michiel J. L. Hayashizaki, Yoshihide Usui, Kengo Harbers, Matthias Research Article Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download. Public Library of Science 2016-02-10 /pmc/articles/PMC4749234/ /pubmed/26863543 http://dx.doi.org/10.1371/journal.pone.0146950 Text en © 2016 Kimura et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Kimura, Yasumasa Soma, Takahiro Kasahara, Naoko Delobel, Diane Hanami, Takeshi Tanaka, Yuki de Hoon, Michiel J. L. Hayashizaki, Yoshihide Usui, Kengo Harbers, Matthias
spellingShingle	Kimura, Yasumasa Soma, Takahiro Kasahara, Naoko Delobel, Diane Hanami, Takeshi Tanaka, Yuki de Hoon, Michiel J. L. Hayashizaki, Yoshihide Usui, Kengo Harbers, Matthias Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays
author_facet	Kimura, Yasumasa Soma, Takahiro Kasahara, Naoko Delobel, Diane Hanami, Takeshi Tanaka, Yuki de Hoon, Michiel J. L. Hayashizaki, Yoshihide Usui, Kengo Harbers, Matthias
author_sort	Kimura, Yasumasa
title	Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays
title_short	Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays
title_full	Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays
title_fullStr	Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays
title_full_unstemmed	Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays
title_sort	edesign: primer and enhanced internal probe design tool for quantitative pcr experiments and genotyping assays
description	Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.
publisher	Public Library of Science
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749234/
_version_	1613536919612817408

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays

Similar Items