Evidence map›Paper›PMID 20040575›Full record

ArticleNucleic acids research2010

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

Open access · goldAbstract read
In one paragraph

Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.

0numbers the graph read from it
0cells of the map it votes in
62citing papers in PubMed
1.9field-weighted citation impact, top 14% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

62 citing papers in PubMed, 107 citations in OpenAlex.

  1. Review
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  15. MAEBL Contributes toInternational journal of molecular sciences · 2022
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  17. Enhanced Prodigiosin Production inApplied and environmental microbiology · 2021
    Article
  18. pLannotate: engineered plasmid annotation.Nucleic acids research · 2021
    Article
  19. Article
  20. Self-assembled mRNA vaccines.Advanced drug delivery reviews · 2021
    Review

2 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 3 institutions in 2 countries.

Ronald GodiskaLucigen Corp., 2120 W. Greenview Dr., Middleton, WI 53562, USA. rgodiska@lucigen.com
David Mead
Vinay Dhodda
Chengcang Wu
Rebecca Hochstein
Attila Karsi
Karen Usdin
Ali Entezam
Nikolai Ravin
Mississippi State University · USRussian Academy of Sciences · RULucigen Corporation · US

Funding

Understanding the mutational mechanism responsible for the Repeat Expansion DiseasesZIADK057808 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI USDIN, KAREN P. · 2009 to 2025
$14.1M
High Fidelity Genomic Cloning and AmplificationR44HG003076 · NHGRI · LUCIGEN CORPORATION · PI GODISKA, RONALD · 2006 to 2007
$824k
High Fidelity Genomic Cloning And AmplificationR43HG003076 · NHGRI · LUCIGEN CORPORATION · PI GODISKA, RONALD · 2003 to 2003
$100k
NHGRI NIH HHS 5R44 HG003076-03NHGRI NIH HHS R43 HG003076
6 · The paper itself

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.

Indexed as

Genetic VectorsMicrosatellite RepeatsAT Rich SequenceBase SequenceCloning, MolecularDNADNA Repeat ExpansionEscherichia coliGenomic LibraryPlasmidsDNA

Identifiers

PMID20040575
PMCPMC2847241
OpenAlexW2142377280

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.