Wikipedia:Good article reassessment/Oligonucleotide synthesis/1

Oligonucleotide synthesis

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

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Article (edit | visual edit | history) · Article talk (edit | history) · Watch • Watch article reassessment page • GAN review not found

Result: Delisted. —Femke 🐦 (talk) 19:21, 19 February 2023 (UTC)

As per usual, some uncited material including

• The DMT group is removed with a solution of an acid, such as 2% trichloroacetic acid (TCA) or 3% dichloroacetic acid (DCA), in an inert solvent (dichloromethane or toluene). The orange-colored DMT cation formed is washed out; the step results in the solid support-bound oligonucleotide precursor bearing a free 5'-terminal hydroxyl group. It is worth remembering that conducting detritylation for an extended time or with stronger than recommended solutions of acids leads to depurination of solid support-bound oligonucleotide and thus reduces the yield of the desired full-length product.
• The reaction is also highly sensitive to the presence of water, particularly when dilute solutions of phosphoramidites are used, and is commonly carried out in anhydrous acetonitrile. Generally, the larger the scale of the synthesis, the lower the excess and the higher the concentration of the phosphoramidites is used. In contrast, the concentration of the activator is primarily determined by its solubility in acetonitrile and is irrespective of the scale of the synthesis. Upon the completion of the coupling, any unbound reagents and by-products are removed by washing.
• The First commercially available oligonucleotide synthesizers section (there's a weird external link in the middle of it)
• (2) The second approach is only used when the intended method of purification is reverse-phase HPLC. In this case, the 5'-terminal DMT group that serves as a hydrophobic handle for purification is kept on at the end of the synthesis. The oligonucleotide is deprotected under basic conditions as described above and, upon evaporation, is purified by reverse-phase HPLC. The collected material is then detritylated under aqueous acidic conditions. On small scale (less than 0.01–0.02 mmol), the treatment with 80% aqueous acetic acid for 15–30 min at room temperature is often used followed by evaporation of the reaction mixture to dryness in vacuo. Finally, the product is desalted as described above. For some applications, additional reporter groups may be attached to an oligonucleotide using a variety of post-synthetic procedures.

And more. These will have to be cited in order to remain a GA. Onegreatjoke (talk) 22:15, 7 February 2023 (UTC)

Pinging Chemist234 who nominated the article for GA in 2009. It's not clear if it got much of a GAN review at the time, so I'm not sure how much work would be needed to get it up to the criteria. But if C234 is still interested/able, perhaps they can deal with your notes above. Ajpolino (talk) 22:44, 7 February 2023 (UTC)

Just a few comments from someone who has not worked on this article and who is indebted to those that have done so much fine work on an important topic:

• • Statements like "...with a solution of an acid, such as 2% trichloroacetic acid (TCA) or 3% dichloroacetic acid (DCA), in an inert solvent (dichloromethane or toluene). The orange-colored DMT cation formed is washed out; the step results in the solid support-bound oligonucleotide precursor bearing a free 5'-terminal hydroxyl group." seems too detailed for encyclopedia.
  • Phrases like "It is worth remembering", "recommend" may be in conflict with WP:NOTMANUAL and/or WP:NOTTEXTBOOK.
  • Article is too heavy on primary references, many of which have been summarized in secondary references WP:SECONDARY and, in the case of this mature area, WP:TERTIARY. Large numbers of primary references put off readers and suggest the absence of any editor with an overview of the topic.
  • Article cites several patents. At least in Wikipedia:WikiProject Chemistry, we rarely cite patents. They are not peer-reviewed, they are often narrow. Most chem editors question whether they are RS.
  • Article uses the term "recent" several time. That adjective becomes stale with time.
  • Artcile uses the term "very" often. Such intensifiers lose their impact after multiple uses.
  • The section "Characterization" is sorta generic and not very interesting (to me at least).
  • --Smokefoot (talk) 23:39, 7 February 2023 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.