Difference between revisions of "DNA/Assembly"

Latest revision as of 19:19, 28 June 2017

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BioBrick cloning sites

To adhere to the BioBrick standard for physical composition of genetic parts, plasmid backbones must include a BioBrick cloning site. The cloning site includes a BioBrick prefix sequence composed of an EcoRI, NotI, and XbaI restriction enzyme recognition site and a BioBrick suffix sequence composed of a SpeI, NotI, and PstI restriction enzyme recognition site.

In most BioBrick plasmid backbones, including those constructed from the BioBrick base vector, the BioBrick prefix and suffix sequences are not adjacent to one another. Instead, the BioBrick prefix and suffix flank what is a called a default plasmid insert or default insert for short. There are several different default inserts available in the Registry. See default plasmid inserts for more information.

There are no parts for this table

Other cloning sites

Some plasmid backbones available in the Registry adhere to other standards for physical composition or simply have multiple cloning sites typical of most molecular biology vectors. Parts encoding non-BioBrick cloning sites are listed here.

BioBrick restriction enzyme sites

The BioBrick standard for physical composition includes the EcoRI, NotI, XbaI, SpeI, and PstI restriction sites. Parts encoding each of the BioBrick restriction enzyme sites are listed here.

There are no parts for this table

BioBrick scars

When a BioBrick part digested with EcoRI and SpeI is assembled with a BioBrick parts digested with XbaI and PstI, the partial SpeI and XbaI sites combined to form a mixed site or scar that cannot be cut by either SpeI or XbaI. A part encoding the BioBrick scar sequence is listed here.

There are no parts for this table

BioScaffold sites

Bioscaffold sites are BioBrick parts that contain restriction enzyme recognition sites that enable full or partial removal of the Bioscaffold site from a composite BioBrick part. Bioscaffold parts address some of the limitations of BioBrick standard assembly by enabling protein fusions, cloning of part libraries within a composite BioBrick part, and removal of BioBrick scars.

Julie Norville, as a graduate student in Tom Knight and Angie Belcher's lab at MIT, developed a new set of DNA parts called Bioscaffold sites. Bioscaffold sites can be assembled as regular BioBrick parts, but enable you to remove BioBrick scars, create protein fusions, and insert part libraries within composite parts.

To learn more about BioScaffold sites, also see Help:Assembly_standard_15.

References

1. [http://openwetware.org/wiki/The_BioBricks_Foundation:BBFRFC15 BioBricks Foundation RFC 15] by Julie Norville, Angie Belcher and Tom Knight

BioBrick-compatible restriction enzyme sites

Some restriction enzymes produce DNA ends that are compatible with the DNA ends produced by the BioBrick restriction enzymes. These BioBrick compatible restriction enzyme sites are useful for certain applications, such as building BioBrick vectors. We list the parts encoding those restriction enzymes sites here.

There are no parts for this table

BioBrick-compatible scars

When a DNA fragment digested with a BioBrick enzyme is assembled with a second DNA fragment digested with a BioBrick-compatible enzyme, the ligated DNA forms a mixed site or scar. Parts encoding the possible scars from BioBrick-compatible sites are listed here.

There are no parts for this table

Other restriction enzyme sites

Parts encoding miscellaneous restriction enzyme sites, including those used in other physical composition standards, are listed here. Rich Roberts, who won the Nobel Prize in Physiology or Medicine in 1993 for his work on restriction enzymes, maintains a restriction enzyme database at http://rebase.neb.com.

Other scars

Other possible mixed sites or scars are listed here.

Single nucleotides

When specifying composite BioBrick parts, it can be helpful to sometimes specify a single nucleotide within the composite part. Thus, parts encoding each nucleotide alone are listed for convenience.