Chemical DNA Synthesis Cycle Chart

This chart describes the steps and detailed mechanisms involved in oligonucleotide synthesis. Initially a reference tool for the Stanford Genome Technology Center Oligo Facility, the chart is now available for public use. The idea behind this updated version of the chart was to consolidate all pertinent aspects of the cycle, including side reactions, in to one convenient location, with the sole purpose of educating anyone interested in chemical DNA synthesis.

What also makes this cycle unique is the interactive element, which allows the viewer to click on/open certain links that reference journal articles further detailing the chemistry/research of that particular step/mechanism. The articles are accessible for immediate viewing through PDF files, so the viewer does not have to hunt around third party websites for this information. Also, each step has an associated thumbtack, that if the mouse pointer is placed over it, a dialog box appears detailing that particular step.


Michael A. Jensen
m.a.jensen at stanford dot edu


Mike Jensen (SGTC)
Hugh Mackie (Glen Research)
Laurent Jaquinod (CTGen)

Chemical DNA Synthesis Cycle Chart.
PDF without attachments, 921 KB
[open in this window]
[open in a new window]

Chemical DNA Synthesis Cycle Chart.
PDF with attachments, 5.02 MB[open in this window]
[open in a new window]

Adobe Acrobat Reader is required to see the attachments.
Because this interactive chart is still in the beta phase, any suggestions/comments are welcome to improve the accuracy and expansion of its material. Though a number of journal articles have already been added to the chart for starters, this is by no means the extent of literature available. It is the hopes of this author that outside researchers familiar with this cycle will suggest additional articles where applicable. The chart will be updated periodically to reflect these changes.

  1. Albericio, A. (2000) Solid-phase Synthesis: A Practical Guide
  2. Khudyakov, Y.E. and Fields, H.A. (2003) Artificial DNA: Methods and Applications
  3. Blackburn, M.G., Gait, M.J., Loakes, D. and Williams, D.M. (2006) Nucleic Acids in Chemistry and Biology
  4. Behlke, M.A. and Devor, E.J. (2005) Chemical Synthesis of Oligonucleotides

This chart is for public viewing only, and should be credited accordingly if it is in anyway referenced in a publication. Please contact the author if you have any questions/comments or wish to obtain a copy for educational purposes only.
Contact: m.a.jensen at stanford dot edu