I am trying to understand the function and purpose of some of the parts of a plasmid. Could someone please explain the following terms:

 

Long Terminal Repeats

 

5' and 3' UTR (untranslatable regions)

 

left and right homology arms

Hi! I will try to answer your question.

 

These parts (U3-R-U5) form part of LTR, which are as you have said Long Terminal Repeats. Well, they are related to retrovirus and retrotransposons (in case you wanted to learn more). You can use them in a plasmid as a good promotor, especially for eukaryotic cells. Second, 5' and 3' UTR are regions inside mRNA that are no translated (this is to say that they are transcribed but not translated, so they will not form part of the protein). Finally, homology means "equal" in biology, and it is a quality. Then, it means something like they are completely identical, both left and right arm.

 

I hope you find it useful!

 

Best regards from Spain!

Thank you so much for your response. It is helpful. But what is the purpose of homology arms in general during construct design. What purpose do they serve aside from them being equal? Do they convey some sort of specificity?

 

On that same note, what are LTRs used for in construct design and are they the physical promotor? I always thought that you add the promoter at the end of the 5' LTR? Thanks again.

Well if they are homolgous you can take advantage of it since you can force them to recombinate, so for example you do not need to use restriction enzymes and ligases in order to insert the fragment inside the chromosome's host (or another vector). This method will let you to insert everything that is present between the two arms. If I'm not wrong you have to use a recombinase for this.

 

LTRs, as I told you before, are present for example in retrovirus, and they use this promoter for its developing cycle. LTRs are promotors made up of U3/R/U5, and they contain signals for polyadenilation, for capping (addition of 5' CAP), etc. You can use them as a single promotor or you can add another one close to them if you want to "superincrease" the transcription rate.