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CABRI Guidelines for Catalogue Production

Guidelines prepared for CABRI by BCCM, CBS, CERDIC, DSMZ, ECACC, HGMP, INRC, MSDN
Page layout by CERDIC

Data input & authentication Flat file preparation Flat file submission

Plasmids format and reference list: Agreed list for properties and applications of plasmids

This field should contain the complete input value (displayed in bold). The VECAP numbers refer to the publication of Vicente et al., World Journal of Microbiology and Biotechnology 1992; 8:519-526. Note that on the one hand some VECAP numbers have been removed and on the other hand some numbers have been added.

To be indexed by CABRI, and as such searchable: single terms of the complete input value.

  1. General cloning vector (VECAP402)

    2. Vector used for cloning DNA fragments as primary purpose.

  2. Replacement vector (VECAP403)

    3. DNA fragments are cloned allowing substitution of foreign DNA for the non-essential fragment of vector DNA that is flanked by widely spaced sites for a particular restriction enzyme. Only applicable for phage vectors.

  3. Insertion vector (VECAP404)

    4. The genome of the insertion vector is small enough to allow cloning of DNA fragments of limited size (e.g. 10 kb for lambda). The vector has a single site for a restriction enzyme in a non-essential part of its genome. Only applicable for phage vectors.

  4. YAC (VECAP405)

    5. Due to the presence of telomers (TEL), a centromere (CEN) and an element for autonomous replication (ARS), the vector replicates as an artificial yeast chromosome, once a non-essential DNA fragment between the TEL elements has been removed by cleavage of the vector with a restriction-enzyme.

  5. Promoter probe vector (VECAP406)

    6. Can be used for cloning promoters and to monitor promoter activity. The DNA fragment is cloned into a cloning site that is located in front of a relevant reporter gene (possessing a translation initiation region).

  6. Translation initiation probe (VECAP407)

    7. Can be used for cloning translation-initiation signals and analyse their activity. The vector contains a reporter gene without the translation initiation codon, but with an upstream promoter.

  7. Transcription termination probe (VECAP408)

    8. Can be used for cloning transcription terminator sequences into a cloning site that is located in front of a relevant reporter gene. DNA fragments containing terminator sequences can be monitored by a decrease in expression of the reporter gene.

  8. Export signal probe (VECAP409)

    9. Can be used for cloning DNA fragments containing export signal sequences into a cloning site that is located in front of a relevant reporter gene. DNA fragments containing export signal sequences can be monitored by monitoring activity of an exported protein.

  9. Sequencing vector (VECAP410)

    10. Can be used for cloning DNA fragments for the purpose of purifying single stranded DNA and determining its nucleotide sequence.

  10. Epitope mapping (VECAP411)

    11. Intended to mark those vectors that would be used to generate parts or deletions of a gene expressing an antigen, suitable then for producing fragments to map epitopes.

  11. Positive/negative screening vector (VECAP416)

    12. A vector useful to screen for a changed phenotype.

  12. Vector construction (VECAP417)

    13. A plasmid containing gene cassettes, polylinkers or (suicide) ori cassettes flanked by several restriction enzyme sites so that they can be easily isolated and used for vector construction.

  13. Preparation of single-stranded probes (VECAP418)

    14. A vector that can be used to prepare single-stranded DNA.

  14. Preparation of gene banks (VECAP419)

    15. A cloning vector that is suitable for the preparation of gene banks. These can be either libraries that are to be screened with nucleic acid probes, or libraries that are to be screened with immunological probes (expression libraries), to isolate DNA sequences that code for specific antigens.

  15. Oligonucleotide directed site-specific mutagenesis (VECAP420)

    16. A plasmid that allows the introduction of mutations into cloned genes, by methods that all involve the use of enzymes and chemicals that cleave, degrade, or synthesize DNA.

  16. Insertion/deletion mutagenesis (VECAP421)

    17. A plasmid that possesses a gene cassette flanked by convenient restriction-enzyme sites, so that the gene cassette can be easily isolated and used for insertion or deletion mutagenesis of cloned genes.

  17. Chromosomal insertion/deletion mutagenesis (VECAP422)

    18. A vector that can be used to clone (mutated) genes followed by the transfer of these genes to the bacterial chromosome by means of homologous recombination or transposition events.

  18. Dimerization studies (VECAP423)

    19. A plasmid that can be used to investigate dimerization domains in proteins.

  19. Gene probe plasmid (VECAP424)

    20. A plasmid carrying a gene of interest, or part of it, which is not expressed.

  20. Protein production plasmid (VECAP425)

    21. Plasmid expressing a cloned gene of interest, producing a protein.

  21. Protein secretion plasmid (VECAP426)

    22. Plasmid expressing a cloned gene of interest, producing a secreted protein.

  22. Reporter plasmid (VECAP427)

    23. Plasmid carrying a reporter gene to monitoring promoter activity, polycistronic transcripts, binding site dependent inhibition or activation, etc.

  23. Tool plasmid (VECAP428)

    24. An auxilliary plasmid expressing a function which is either required or useful to deploy or optimize the principal function of the primary plasmid (e.g. T7 RNA polymerase, lysozyme, chaperones, etc.).

  24. Transcomplementation of vectors for mobilization (VECAP429)

    25. A conjugation helper plasmid providing the (oriT) transfer functions in trans.

  25. Suicide vector: Transposon delivery (VECAP501)

    26. A suicide plasmid that possesses all information for transposon delivery (transposase, Tn marker, IS sequences).

  26. Suicide vector: Conditional replication (VECAP502)

    27. A suicide vector that can only replicate in E. coli when certain replication functions (like lambda pir) are provided by the host. These vectors can be used as a suicide vector in E. coli, not expressing these functions, too.

  27. Suicide vector: Recombination vector (VECAP503)

    28. A suicide vector in which genes can be cloned.

  28. Expression vector: general expression (VECAP601)

    29. A cloning vector that can be used for gene expression.

  29. Expression vector: secretion vector (VECAP602)

    30. A cloning vector that can be used for gene expression and protein secretion, providing a heterologous promoter, translation initiation region and a signal sequence.

  30. Expression vector: heterologous promoter (VECAP603)

    31. A cloning vector that can be used for gene expression, providing a heterologous promoter.

  31. Expression vector: heterologous translation initiation region (VECAP604)

    32. A cloning vector that can be used for gene expression, providing a heterologous translation initiation region.

  32. Expression vector: heterologous messenger stability determinant (VECAP605)

    33. A cloning vector that can be used for gene expression, providing a heterologous messenger stability determinant.

  33. Expression vector: in vitro expression: fusion protein (VECAP606)

    34. A cloning vector that can be used for gene expression by creating translational fusions to the 3'or 5' end of a gene.

  34. Expression vector: in vitro expression: proteolytic site (VECAP607)

    35. A cloning vector that can be used for gene expression by creating translational fusions to the 3'or 5' end of a gene, and that enables site-specific proteolysis of fusion proteins.

  35. Expression vector: recombinant protein purification (VECAP608)

    36. A cloning vector designed for the expression of cloned genes and providing a convenient method for purifying a (biological active) gene product.
 
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