User:Chris D Hirst/Plasma

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Contents

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 BBa prefix and BBa suffix!

Import a vector containing BBa E0240 from this .pof file


Restriction Enzyme, ORF and Primer Binding Analysis



Cloning - Biobricks RFC 10 (BBa)



Analysis of cloning results



Cloning - PCR and Biobrick (BBa)



Cloning - Infusion



Exporting



References


  1. Angers-Loustau A, Rainy J, and Wartiovaara K. . pmid:17868482. PubMed HubMed [1]
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