User:Jarle Pahr/Oligonucleotides

Notes on the synthesis and use of oligonucleotides:

General information

Sigma Alrich - oligonucleotide learning center: http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center.html

Melting temperatures

http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center/oligos-melting-temp.html

Purification, quality control and error rates

http://eu.idtdna.com/pages/support/technical-vault/faq/application-support/synthesis/faqs/2011/06/27/what-is-the-probability-of-finding-an-error-in-my-oligo-what-is-the-percentage-of-truncations-or-deletions-i-can-expect-?c=EU

http://www.synthesisgene.com/tools/oligosynthesis.pdf

Advances in the Synthesis of Oligonucleotides by the Phosphoramidite Approach: http://www.sciencedirect.com/science/article/pii/S0040402001887524

http://dna-9.int-med.uiowa.edu/?q=node/49

According to this page, Phosphoramidite oligo synthesis currently has an error rate of 1 in ~160. This corresponds to a success rate of 0.99375 per step. For a 50-mer synthesis, this would result in ~73 % of products having the correct sequence.

Assuming a success rate of 0.99, a 50-mer would give 61 % correct products.

http://www.abrf.org/index.cfm/list.msg/70715?brSort=thread&listName=abrf&urlStr=

According to this page, "Because truncations are common, and deletions do occur to a much smaller degree, we strongly recommend PAGE purification for any oligo used for cloning, mutagenesis, or other sensitive procedures regardless of oligo length." and "Base substitutions are extremely rare."

IDT technical report: http://eu.idtdna.com/pages/docs/technical-reports/chemical-synthesis-of-oligonucleotides.pdf

Conclusions in brief:

Oligomer synthesis services

Sigma Aldrich: http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/product-lines/standard-synthesis.html

Sigma Aldrich price list: http://www.sigmaaldrich.com/canada-english/sigma-genosys-canada/custom-dna-synthesis.html

http://www.macrogen.com/eng/index/

Hardware

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860119/

Bibliography

http://www.jbc.org/content/288/2/1420.full?sid=8fe58578-5f73-413d-b7c4-d5b88e5ad50a

LeProust E. M., et al. (2010) Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res. http://nar.oxfordjournals.org/content/38/8/2522.full

Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2503.html