User:Chris D Hirst/Plasma
Introduction
PlasmaDNA[1] is a free to use computer programme developed by the University of Helsinki to allow the easy mainpulation of DNA in silico. In the hands of an experience user, it can be used to fully plan out the assembly of a synthetic construct from base parts, genome sequences, cDNAs - basically any DNA input for which a text or FASTA file can be found. The ability to attempt a cloning strategm in silico before going into the lab can help identify bottlenecks and critical paths while allowing the user to visually see what they are producing.
While other programmes can do this, PlasmaDNA is free, very use friendly and produces highly detailed plasmid maps in 3 flavours. Some lab members already create PlasmaDNA (.pof) files for all the vectors and constructs they build. This and the ability to visualise cloning can prove very useful to aid understanding and debug when issues arise.
PlasmaDNA can be accessed here.
Tutorial
If you follow this tutorial, you should be able to use most of the features of PlasmaDNA. If you get stuck at any point, try having a play around with the programme! Most difficulties can easily be solved by trial and error. If you don't understand what you are doing, let me know and I'll help you.
Importing Sequences
PlasmaDNA can import sequences in one of three formats: Plain text, FASTA (similar to plain text) and .pof (Plasma) files.
To start off this tutuorial, load the sequence of BBa R0062 (from the parts registry) and remember to add the BioBrick prefix and suffix!
Import a vector containing BBa E0240 from this .pof file
Restriction Enzyme, ORF and Primer Analysis
The Output viewer should already be open. If not, open it (button in the top left of the control panel and look at the output of the two inputs. One should be a complete circular vactor and one should be a short linear piece. The view is currently set to restriction analysis - ie. it shows all the restriction enzyme cutting sites on the sequences. Two alternative viewer modes are ORF analysis - this looks for Open Reading Frames (ie. coding regions) in the sequence according to a user set threshold (default is generally ok) and primer analysis - compares the input sequence to known primer sequences.
There are currently two known ORFs in E0240 and none in R0062, however the ORF analysis function indicates there is an extra coding region here. Determine the nature of the coding region - either by part knowledge or using the blast function in the ORFs menu and add it to the current project.
Add the primers from this text file to this project on PlasmaDNA (using the add primer button not enter sequence button), then look at the two outputs under primer analysis. Can you suggest a use for SeqF and SeqR?
Restriction Cloning - Biobricks RFC 10 (BBa K116617)
Analysis of cloning results
3A Assembly - PCR and Biobricks (BBa F2622)
Oh no! You've attempted to get BBa F2622 from the registry plate and succesfully transformed the cells but upon gel analysis it appears that all your transformants contain an empty plasmid!
Luckily you find that BBa I0462 and BBa R0011 are correct upon prepping from the registry, though R0011 for some reason is in plasmid pSB1AK3 not pSB1A2.
For easy selection of correct transformants you decide it would be better to transform into a vector with a resistance other than Amp or Kan so choose to use 3A Assembly.
Cloning - Infusion
Exporting
References
