The Hitachi Software MiraiBio Group Blog

1. A job queuing system was implemented - You no longer need to wait for compute-intensive results (e.g. BLAST searches on multiple sequences) to come back. Just submit a job and continue working. When the results are in, you’ll be notified.

2. You can now add comments to tools and read other users’ comments. See what your colleagues have to say about which tools are best for a given task, or if there’s any tips and tricks to get the most value from a tool.

3. Auto-scrolling to results has been fixed - When you click on a result in the left pane, the right pane will automatically scroll to the corresponding position on the page so you can instantly access any result.

4. More help features to guide new users - You’ll notice several new icons to help you use SmartNote’s features.

5. Other cool additions such as the new animated progress icon for the sequence manager window.

6. Many bug fixes - everything just works more smoothly.

Remember to tell us what you think about DNASIS SmartNote and what new features you’d like to see. We’ve been making changes weekly, so as long as your request is reasonable, we’ll most likely be able to add it.

By default, DNASIS SmartNote will track PubMed articles related to up to 10 of your most recently imported sequences. You can view these regularly updated articles by clicking on the “Articles” tab. From here, you can also clip individual articles into your notebook, as well as print and email them.

If you want to receive regular email updates for new articles, you’ll need to explicitly mark at least one of your sequences listed in the “My Seq’s” tab. You will then start receiving regular emails with any newly published articles related to your sequences. Since you can only track 10 sequences, the sequences you have explicitly marked will get higher priority.

How does DNASIS SmartNote find related articles? If the sequence was imported as a GenBank file, DNASIS SmartNote looks for gene names in the annotations. Otherwise, it defaults to a plain text search of words in the sequence’s description.

We invite you to try out this new feature and let us know if we can do anything to improve it for you.

Since PCR primer design is one of the most widely used features of DNASIS SmartNote, we did some research and put together a list of the top 10 tips for designing PCR primers that work. When designing oligonucleotide primers for PCR, it is helpful to keep some considerations in mind to optimize the output and specificity of your experiment. Here are some tips gathered from experts to get you started:

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