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
Purification, quality control and error rates
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