What can SmartNote offer to you?

• SmartNote has many analysis tools including popular tools such as Blast, ClustalW, Primer3 and much much more. You can run a single analysis on one sequence or save time by running a batch analysis on multiple sequences. If you don’t see a tool that you would like, then just request it and we will try our best to add it as soon as we can.
• You can easily share sequences, results, pages, and even your entire notebook with colleagues.
• Store and organize your sequences using our tagging system to find them easily later on.
• Track articles for your sequences. Do you find yourself constantly looking for new articles related to the sequences you are working on? Now, you can sit back and relax and let SmartNote automatically do it for you.

We are only skimming the surface here. If you are interested in the full potential of SmartNote and what it can do for you, then check it out for yourself!

1. Design your PCR primers to be 18-30 oligo nucleotides in length. The longer end of this range allows higher specificity and gives you space to add restriction enzyme sites to the primer end for cloning.

2. Make sure the melting temperature (Tm) of the primers used are not more than 5°C different from each other. You can calculate Tm with this formula: Tm = 4(G + C) + 2(A + T)°C

3. Aim for a Tm between 65 and 70°C for each primer over the region of hybridization

4. Use an annealing temperature (Ta) of 10 to 15°C lower than the Tm.

5. The GC content of each primer should be in the range of 40-60% for optimum PCR efficiency.

6. Try to have uniform distribution of G and C nucleotides, as clusters of G’s or C’s can cause non-specific priming.

7. Avoid long runs of the same nucleotide.

8. Check that primers are not self-complementary or complementary to the other primer in the reaction mixture, as this will encourage formation of hairpins and primer dimers and will compete with the template for the use of primer and reagent.

9. If you can, make the 3′ end terminate in C or A, as the 3′ is the end which extends and neither the C or A nucleotide wobbles. This will increases the specificity.

10. You can avoid mispriming by making the 3′ end slightly AT rich.

11. Use the right software. OK, so it’s 11 tips. Using the right software is a great way to automate these steps and minimize errors, especially when you have to design primers for many sequences. DNASIS SmartNote includes several primer design tools and is also a lab notebook that automatically keeps a record of your analysis results. You should definitely give it a try. Click here to sign up a free account.

If you prefer traditional desktop software, take a look at DNASIS Max instead.

References:

http://rothlab.ucdavis.edu/protocols/PrimerDesign.html

http://www.biochem.ucl.ac.uk/bsm/nmr/protocols/protocols/oligo.html

http://www.protocol-online.org/prot/Molecular_Biology/PCR/PCR_Primer/

http://www.mcb.uct.ac.za//pcroptim.htm

Congratulations to Boris Zinshteyn for winning the Top Feedback prize of a $25 Amazon.com gift certificate! We still have plenty of gift certificates available, so please take a couple of minutes to tell us what you think about DNASIS SmartNote and especially how we can improve it for you.

1. You can now export individual results (summaries or raw) from your lab notebook as PDF files or print them out.

2. The PrimerX tool has been added to support primer design for mutagenesis. It even works with multiple sequences!

3. You can now extract email addresses from your GMail or Yahoo mail accounts to make it easier to invite your colleagues to collaborate with you through DNASIS SmartNote.

4. If you find yourself using the same tools frequently, you’ll love this feature: when it’s time to pick a tool for an analysis, you can now see the 5 most recently used tools listed at the very top and just click them to quickly launch the analysis.

Coming soon… an exciting new way to share data with colleagues!

Some users said they needed more help getting started using it. This is not surprising, since DNASIS SmartNote’s design is innovative in two ways – it’s a meta-application (an application that uses other applications) and it’s also the first bioinformatics tool we know of that combines a lab notebook, sequence analysis and social networking.

Others said they want to be able to import sequences in formats other than FASTA. I’m happy to report that GenBank support will soon be available on the live site.

Finally, we are starting to get requests to support specific workflows, such as designing primers for mutagenesis. One user suggested adding a view that shows both DNA and protein sequences. We would love to hear from other DNASIS SmartNote users so we know where to focus our efforts to best meet users’ needs. So please send us feedback or post to this shared blog. Together, we can make DNASIS SmartNote even better!

Use this blog to post:

• protocols and get help troubleshooting your experiments
• experiment results from your lab notebook that you want to share and invite others to comment on- relevant events, shows and conferences
• hot topics in life science research- job postings
• ideas for how to improve SmartNote
• anything else of potential interest to the community of SmartNote users

Then, invite your colleagues to read and comment on your posts. The most popular posts will automatically be listed on this page, so you can easily access the information that others find most useful or interesting.So go ahead and get started!