What is PlasmaDNA?
PlasmaDNA is a DNA analysis and manipulation software designed in particular to facilitate the planning and archiving of cloning experiments.
Most molecular and cellular biology experiments, and the techniques associated with this field, involve a great deal of engineering in the form of the manipulation of DNA sequences. Like all forms of engineering, very accurate information is crucial for successful design and implementation of strategies.
In 2007, the freeware PlasmaDNA was released, available both on Windows and Apple operating systems, designed to facilitate molecular cloning experiments by building a visual map of the DNA. It then allows the complete planning and simulation of the cloning experiment, automatically updating the new sequences generated in the process. The capacity to maintain the link between the multiple sequences can also be used to archive the various steps and strategies involved in the generation of each construct.
The program can be downloaded for free from a site hosted at the University of Helsinki (note: the page is no longer available; the software can still be downloaded from here)
It has been the subject of an open-access publication: Angers-Loustau et al, 2007
The PlasmaDNA.net website was released in 2012 to complement and build upon the existing tool.
Using this web application requires the creation of an account, and adds the following advantages:
- Easy access to the application from anywhere, including from 3G-enabled tablets. The site has been optimised to use very little data, in part by using Scalable Vector Graphics (SVGs) as the graphical format for the plasmid maps. For example, the drawing above is only 5kb despite the high resolution.
- Remote storage of the saved files on PlasmaDNA.net, for easy access of the saved work from anywhere. This includes all domains and primers databases, as well as all the saved fragments. The PlasmaDNA.net is compatible with the files generated by the PlasmaDNA program, and it possible to upload all the existing work to the your account and keep working where you left. All the files can also be downloaded to be used with the PlasmaDNA program.
- Regular updates of PlasmaDNA.net will not require keeping installed versions up-to-date, the user always has access to the latest improvements of the application.
In addition, the web application is regularly updated to add functionality which does not exist in the older program. So far, this includes:
- Capacity to print the maps directly from PlasmaDNA.net at high resolution.
- Capacity to include restriction enzymes, primers and domains with degenerate bases.
- Capacity to click directly on the elements of the maps to see more information.
- Capacity to customize the colours in the fragment drawings
Creating an account and using the application is free, so come take a look!
Good luck with your experiments,
Alexandre Angers-Loustau and Ana-Maria Osiceanu