Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli

Ronald Godiska, David Mead, Vinay Dhodda, Chengcang Wu, Rebecca Hochstein, Attila Karsi, Karen Usdin, Ali Entezam, Nikolai Ravin

Research output: Contribution to journalArticlepeer-review

66 Scopus citations

Abstract

Despite recent advances in sequencing, complete finishing of large genomes and analysis of novel proteins they encode typically require cloning of specific regions. However, many of these fragments are extremely difficult to clone in current vectors. Superhelical stress in circular plasmids can generate secondary structures that are substrates for deletion, particularly in regions that contain numerous tandem or inverted repeats. Common vectors also induce transcription and translation of inserted fragments, which can select against recombinant clones containing open reading frames or repetitive DNA. Conversely, transcription from cloned promoters can interfere with plasmid stability. We have therefore developed a novel Escherichia coli cloning vector (termed 'pJAZZ' vector) that is maintained as a linear plasmid. Further, it contains transcriptional terminators on both sides of the cloning site to minimize transcriptional interference between vector and insert. We show that this vector stably maintains a variety of inserts that were unclonable in conventional plasmids. These targets include short nucleotide repeats, such as those of the expanded Fragile X locus, and large AT-rich inserts, such as 20-kb segments of genomic DNA from Pneumocystis, Plasmodium, Oxytricha or Tetrahymena. The pJAZZ vector shows decreased size bias in cloning, allowing more uniform representation of larger fragments in libraries.

Original languageEnglish (US)
Article numbergkp1181
Pages (from-to)e88.1-e88.9
JournalNucleic acids research
Volume38
Issue number6
DOIs
StatePublished - Dec 29 2009

Bibliographical note

Copyright:
Copyright 2010 Elsevier B.V., All rights reserved.

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