Vectors

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This page contains various information relating to vectors used in OpenWetWare labs.

Contents

General information

Stringent vs. relaxed replication

Plasmid replication control is usually controlled by balancing the levels of a positive and a negative regulator of replication. For some plasmids (pMB1/colE1 replicons) the positive regulator is an RNA and in others (e.g. pSC101) it is a protein. Plasmids with a protein positive regulator will not replicate in the abscence of protein production - stringent control (although not the same as the stringent response due to a shortage of loaded tRNAs). Plasmids with an RNA positive regulator will continue to replicate in the abscence of protein production. This is termed relaxed control. High yields of plasmid may be obtained by halting protein production (via chloroamphenicol) when the culture reaches a high density and then continuing incubation for a number of hours. This might be of practical relevance when prepping the 1 and 3 series of Synthetic Biology plasmids.--BC 19:05, 3 Sep 2005 (EDT)

Online Vector Databases

You can often find vector information at NCBI, either directly or in their list of vectors screened for contamination of new sequence at Vecscreen.

VectorDB contains information about many common vectors, including yeast vectors.

EMBL maintains a large database of vectors.

For eukaryotic vectors (Fish, Xenopus) see Minnesota.

The Forsburg Lab maintains a list of Fisson Yeast vectors.

Promega maintains a list of their vectors.

NEB maintains a list of common vectors.

Epicentre also maintains its own list.

Addgene's Vector DB contains most of the information from Stanford's VectorDB, plus more vector information they have curated from commercial websites and added through our plasmid curation efforts. (However, it seems to be rather sparse when it comes to Escherichia coli vectors.) Note that Addgene is a a non-profit plasmid repository where scientists can archive and share their plasmids. They encourage and invite labs to deposit plasmids at Addgene. They help you with data submission and all tech transfer issues. Plasmids can be requested from Addgene for a fee to cover expenses.

Annotation

PlasMapper: "automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format." It can also output GenBank format. Reference: Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart "PlasMapper: a web server for drawing and auto-annotating plasmid maps" Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.

  • One drawback to this tool is that although it finds ORFs, it doesn't necessarily identify them. -- RS

Also check out APe, A Plasmid Editor.

Escherichia coli

Nomenclature

Available

To be constructed

BioBrick Parts for Plasmid Engineering

Bacterial artificial chromosomes

pSCANS genbank vector info cookbook

Replicon Compatibility

The following are groups of replicons that can be used with the bold replicon in the one cell.

  • colE1 - p15A,R6K, and F
  • pMB1 - p15A,R6K, and F
  • ??

Some sets of vectors with compatible origins are available as a part of the Novagen Duet system. (from TK)

Genbank entries

Note: searching for cloning vector <insert vector name> when looking for vector sequences in NCBI Entrez Nucleotide search. It helps to cut down on the number of hits.

Yeast

Nomenclature and types

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