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The use of multiple displacement amplification to amplify complex DNA libraries

Complex libraries for genomic DNA and cDNA sequencing analyses are typically amplified using bacterial propagation. To reduce biases, large numbers of colonies are plated and scraped from solid-surface agar. This process is time consuming, tedious and limits scaling up. At the same time, multiple di...

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Detalles Bibliográficos
Autores principales: Fullwood, Melissa J., Tan, Jack J. S., Ng, Patrick W. P., Chiu, Kuo Ping, Liu, Jun, Wei, Chia Lin, Ruan, Yijun
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275127/
https://www.ncbi.nlm.nih.gov/pubmed/18285362
http://dx.doi.org/10.1093/nar/gkn074
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author Fullwood, Melissa J.
Tan, Jack J. S.
Ng, Patrick W. P.
Chiu, Kuo Ping
Liu, Jun
Wei, Chia Lin
Ruan, Yijun
author_facet Fullwood, Melissa J.
Tan, Jack J. S.
Ng, Patrick W. P.
Chiu, Kuo Ping
Liu, Jun
Wei, Chia Lin
Ruan, Yijun
author_sort Fullwood, Melissa J.
collection PubMed
description Complex libraries for genomic DNA and cDNA sequencing analyses are typically amplified using bacterial propagation. To reduce biases, large numbers of colonies are plated and scraped from solid-surface agar. This process is time consuming, tedious and limits scaling up. At the same time, multiple displacement amplification (MDA) has been recently developed as a method for in vitro amplification of DNA. However, MDA has no selection function for the removal of ligation multimers. We developed a novel method of briefly introducing ligation reactions into bacteria to select single insert DNA clones followed by MDA to amplify. We applied these methods to a Gene Identification Signatures with Paired-End diTags (GIS-PET) library, which is a complex transcriptome library created by pairing short tags from the 5′ and 3′ ends of cDNA fragments together, and demonstrated that this selection and amplification strategy is unbiased and efficient.
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spelling pubmed-22751272008-04-07 The use of multiple displacement amplification to amplify complex DNA libraries Fullwood, Melissa J. Tan, Jack J. S. Ng, Patrick W. P. Chiu, Kuo Ping Liu, Jun Wei, Chia Lin Ruan, Yijun Nucleic Acids Res Methods Online Complex libraries for genomic DNA and cDNA sequencing analyses are typically amplified using bacterial propagation. To reduce biases, large numbers of colonies are plated and scraped from solid-surface agar. This process is time consuming, tedious and limits scaling up. At the same time, multiple displacement amplification (MDA) has been recently developed as a method for in vitro amplification of DNA. However, MDA has no selection function for the removal of ligation multimers. We developed a novel method of briefly introducing ligation reactions into bacteria to select single insert DNA clones followed by MDA to amplify. We applied these methods to a Gene Identification Signatures with Paired-End diTags (GIS-PET) library, which is a complex transcriptome library created by pairing short tags from the 5′ and 3′ ends of cDNA fragments together, and demonstrated that this selection and amplification strategy is unbiased and efficient. Oxford University Press 2008-03 2008-02-19 /pmc/articles/PMC2275127/ /pubmed/18285362 http://dx.doi.org/10.1093/nar/gkn074 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Fullwood, Melissa J.
Tan, Jack J. S.
Ng, Patrick W. P.
Chiu, Kuo Ping
Liu, Jun
Wei, Chia Lin
Ruan, Yijun
The use of multiple displacement amplification to amplify complex DNA libraries
title The use of multiple displacement amplification to amplify complex DNA libraries
title_full The use of multiple displacement amplification to amplify complex DNA libraries
title_fullStr The use of multiple displacement amplification to amplify complex DNA libraries
title_full_unstemmed The use of multiple displacement amplification to amplify complex DNA libraries
title_short The use of multiple displacement amplification to amplify complex DNA libraries
title_sort use of multiple displacement amplification to amplify complex dna libraries
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275127/
https://www.ncbi.nlm.nih.gov/pubmed/18285362
http://dx.doi.org/10.1093/nar/gkn074
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