DNA Methylation and HydroxymethylationTools & Technology

Everything Starts with Good Primers

As “The Epigenetics Company”, Zymo Research Corporation is dedicated to developing and providing the most comprehensive set of tools for epigenetics research available. With this in mind, we provide on our website the Bisulfite Primer Seeker design program for the quick and easy generation of primers necessary for the PCR amplification of bisulfite converted DNA during methylation analysis.  Ever since Zymo Research launched Bisulfite Primer Seeker in January, it has received over one thousand primer design requests.  Hundreds of scientists used Bisulfite Primer Seeker, and many of them returned to use it again.  The first version was a great success, but we were not satisfied and knew we could do even better.  We listened to user feedback and worked hard to improve the Bisulfite Primer Seeker tool.  Today, we are happy to introduce the next generation of Bisulfite Primer Seeker.

When launching Bisulfite Primer Seeker 12S for the first time, the most significant change you will see is that it has a whole new look.  It keeps the same layout but adds new features that make it more visually pleasing.  We believe that the user interface of scientific tools does not need to be boring, even if the tools are totally free.

The most advanced component of the new Bisulfite Primer Seeker 12S is the ability to search for primers with no CpG dinucleotides in the first third of their sequence.  The previous version of Bisulfite Primer Seeker required that primers be allowed one CpG to give the tool a greater chance of finding good pairs.  However, many scientists also told us they wanted to search for primers with no CpGs.  No problem!  In Bisulfite Primer Seeker 12S, simply uncheck the “Allow 1 CpG in the first 1/3 of primer” box and you can search for primers without CpGs.

In the first version of Bisulfite Primer Seeker you could easily see the CpGs because they were highlighted in the Preview section, but we knew we could make CpGs even easier to detect.  A whole new CpG Preview Bar is added to Bisulfite Primer Seeker 12S.   The new feature includes a green bar representing the user input sequence with all CpGs highlighted in their corresponding positions.  Now visualizing the CpG distribution in your sequence is instantaneous.

We also know that many scientists are interested in the bisulfite converted or the reverse complement of their sequences (and maybe both).  Now you don’t have to use the “replace” function in MS Word, or open other software to do the conversion.  Simply check or uncheck the BS Conversion and Reverse Complement checkbox in the Preview section to get the desired sequence.

Line numbers are useful when analyzing a sequence but can also be annoying if you want to copy and paste the sequence into a word processing application such as MS Word.  The new Line # checkbox feature solves this dilemma.  When you want to copy the annotated sequence, click the Line # checkbox to remove line numbers, and when you need help finding particular nucleotides, simply click the Line # checkbox to bring the line numbers back.

As school starts, don’t forget to try our new Bisulfite Primer Seeker 12S.  It is the most integrated and efficient way to start your methylation journey.


Please email us at services@zymoresearch.com with any questions or feedback on our new Bisulfite Primer Seeker 12S tool.  We hope you find it useful!

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Hunter C.

Hunter C.

Hunter grew up in Taiwan, got his master’s degree in Boston, and now works in southern California. Baseball is his favorite sport, and Hunter plays baseball on the weekends. Hunter loves video games and he has a Lv.50 Witch Doctor and a Lv11 Demon Hunter in Diablo III!