PlasmaDNA helps plan cloning projects with features to do everything from in silico PCR (and gels!) to ORF analysis, restriction/ligation and alignment analysis.

Grad students, you’re about to thank me.

A few weeks ago I found myself in the position of designing my own gene construction project. This normally wouldn’t be such a big deal, but I happen to be one of only a few biologists in a lab primarily consisting of engineers – and of the biologists that are around none are bonafide molecular biologists. I knew all the theory from my courses, but theory and hands-on wet work are very different worlds. So, I was left to my own devices, digging through the Sambrook manuals and reading forum posts. As I slowly gained enough confidence to start purchasing reagents, I found that keeping multiple gene sequences of a few hundred base pairs organized and ensuring that my design will lead to a properly translated protein was rapidly becoming a headache.

Then I found PlasmaDNA. (click the link to download)

It’s difficult to explain all of the many wonderful things about this program, so I’m going to pause for a second and strongly suggest you go download it – it’s free and cross-platform!

Ok, now that you’ve downloaded the program and are enjoying its simple appearance, I suggest you explore. What you’ll need to start, depending on your experimental intents, are (1) a vector sequence, (2) primer sequences and (3) an insert sequence, though this is optional. You’ll find that once you input your FASTA-formatted (or similar) plasmid sequence, you’ll notice right away that the plasmid is beautifully rendered on the screen and, seemingly magically, many of the important regions are automatically identified (origins, resistance genes, restriction sites, tags, and so on). The more you explore, the more wonderful things you will find – for example, when you input primers into a specific sequence “block” and look at the “align” menu, it will overlay the primers onto the sequence and show any overlaps; this was incredibly helpful for visualizing the addition of restriction sites to my gene. I then in silico amplified my gene out of one plasmid, digested the gene and target vector and ligated all within the program! I knew my project would succeed without ever having to touch a pipette or grab my Advil container!

A tip: I recommend accessing the restriction enzyme “menu” and displaying only the enzymes you already have in your lab or are willing to purchase, as seeing all of the sites available for your digests is much more useful than seeing the entire NEB catalog plastered all over your plasmid.

I won’t belabor the point beyond saying that this was easily the best cloning/sequence-focused software I was able to find for free and I would recommend it to anybody in my same situation.

Give it a go and let me know what you think below!

References

• Angers-Loustau, A., Rainy, J. & Wartiovaara, K. PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories. BMC molecular biology 8, 77 (2007). (Source)