Dmt protection is a important step allowing protection of the hydroxyl group in the 5'OH in the nucleotides. This 5'OH specific protection allow a sequential coupling of the nucleotides, forming a obligonucleotide.
As we know DMT protection is follow the sn1 reaction manner. And for sn1 reaction, primary alcohol is less reactive than the secondary alcohol. Therefore, beside steric hindrance I would like to know why DMT is 5'specific. Thank you so much
The dmt is already on the phosphoramidite base on so I wonder if other reactive positions are modified in the synthesis forcing the dmt moiety into its correct position but it does seem likely that the main factor is steric hindrance
5' OH reacts with DMTCl much fast than 3' OH, if you add much more DMTCl or do the reaction at higher temperature, you will also found bis-DMT products, I would not say DMTCl is 5'OH specific.
It can be put on 3'OH too, in case 5'OH is already blocked for purpose!
https://www.biosynth.com/p/PD09188/134031-86-0-3-o-dmt-thymidine-5-ce-phosphoramidi