Help:Plasmid Backbones Archive

What are Plasmid Backbones

You may be familiar with plasmids, circularized DNA that will replicate in cells. Plasmids are extremely useful in molecular biology as they are easily purified from cells, manipulated using common lab techniques and incorporated into cells. Part samples available through the Registry are propagated and maintained on plasmids, however the Registry does not consider plasmids in a traditional sense. Instead of the plasmid as a whole, the Registry divides the plasmid into two separate components: the part sample (functional unit) and the plasmid backbone (which has necessary features to propagate and assemble part samples).

Here we have a part sample (blue) for BBa_R0051 maintained in a chloramphenicol resistant plasmid backbone (green). You can see that the part sample is flanked by the plasmid backbone's prefix (P) and suffix (S), which dictates the part sample's assembly standard.

Each plasmid backbone has its own page on the Registry, including documentation, testing and user experience, just like parts. See pSB1C3 as an example.

Plasmid Backbone Features

The Registry has a variety of plasmid backbones but they all share three common features:

the replication origin is responsible for the replication of plasmids during cell growth and division. Different replication origins can dictate the plasmid copy number per cell (how many molecules of the plasmid are maintained in the cell), mechanism of copy number control, cell-to-cell copy number variation, and even the degree of coiling of the physical DNA.
the antibiotic resistance marker acts as the selective agent for cells that contain your plasmid (the plasmid backbone and your part of interest). In the likely event where some cells have your plasmid and others do not, the antibiotic resistance marker ensures that cells which do not have a copy of the plasmid are killed by the antibiotic present.
the cloning site is the location on the plasmid backbone where part samples are inserted. Cloning sites are divided into two regions, the prefix and suffix, flanking the beginning and end of the part sample, respectively. The specific sequence for the prefix and suffix are dictated by their assembly standard in use. This allows you to easily transfer or assemble part samples from one backbone to another if they belong to the same standard.

Plasmid Backbones in relation too...

Assembly Standards - A plasmid backbone includes a prefix and suffix as defined by the assembly standard. It will also have no restriction sites elsewhere that would interfere with assembly.
Parts - A plasmid backbone propagates a sample of a part, located inbetween the prefix and suffix of the plasmid backbone. As such the plasmid backbone dictates the assembly standard and assembly of that part sample.
Assembly is combining two part samples together in series to form a new composite part. Traditional assembly is done through the use of the plasmid backbone's prefix and suffix (cutting and ligating) as defined by the assembly standard.

Example

The pSB1A2 plasmid backbone has a prefix and suffix as defined by the BioBrick RFC[10] standard. A part sample of BBa_R0051 is flanked by this prefix and suffix.
In order to assemble two different parts you will need to make sure that both part samples are on plasmid backbones belonging to the same assembly standard.

What will I use them for

Plasmid backbones serve many functions for parts:

Packaging for Part Samples: You'll receive your part samples from the Registry in a plasmid backbone. It's expected that you'll take the part samples out of their plasmid backbone packaging and use them accordingly in your experiments. You'll send back new part samples you've made in the pSB1C3 plasmid backbone.

Tools for Assembly: Plasmid backbones also serve to make assembly of part samples easier. You can cut out two part samples from two plasmid backbones and ligate them into a different plasmid backbone to make a new composite part. The Registry offers linearized plasmid backbones to make this process easier.

Note: As mentioned plasmid backbones include the cloning site for a part sample, the prefix and suffix that is defined by a specific assembly standard. This means that the plasmid backbone will also dictate how that part sample will be assembled.

Operation of Parts: You may find that you need a different plasmid backbone to properly operate your part, device, or system, one that uses a lower copy number replication origin so that it doesn't use too many cellular resources.

Other: Plasmid Backbones can serve other purposes: measuring, screening, expression, etc.

Read the plasmid backbones catalog page for more information.

What else do I need to know

Using Parts - How will I transfer my part sample from one plasmid backbone to another?