Protected with a trityl group, e.g., Amino-Modifier C6 (10-1906). Triphenylmethyl groups (trityls) are a popular family of protecting groups, used in oligonucleotide chemistry for hydroxyl (DMT) and amino (MMT) protection, and removable by mild acidic treatment. Conveniently, trityl cations have large extinction coefficients allowing stepwise coupling yields to be measured easily. Alternatively, due to the hydrophobicity of trityls, separation of the full-length product, still bearing the tritylprotecting group, from capped failure sequences can be carried out, with subsequent acidic removal of the DMT or MMT protection as the final step. Manufacturing large numbers of oligonucleotides requires cheap and fast purification techniques, ruling out HPLC and PAGE as too expensive and time-consuming. The popular RP cartridge purification method (e.g., PolyPak) does not allow detritylation of the monomethoxytrityl (MMT) group from protected amino-modified oligonucleotides in high yield on the cartridge.618913-30-7 web The reason for this situation is that acidic cleavage of the N-trityl bond is an equilibrium reaction. On RP cartridge, where the trityl cation is not physically separated from the amine, the process results in substantial (up to 50%) reattachment of the MMT-group back onto the amine. Subsequent elution of the aminomodified oligonucleotide results in a product that is up to 50% inactive. Interestingly, in addition to this reattachment problem, MMT-amino-modified oligos are quite unstable when stored in aqueous ammonia, gradually losing the MMT group over time. Recently, we have seen some interest in the dimethoxytrityl equivalent to the amino-modifier C6, presumably in an attempt to overcome some of the problems associated with the MMT version. In our hands, this phosphoramidite is less stable than its MMT cousin and we have concerns about long-term storage. Although the product couples perfectly well in synthesis, there was substantial loss of DMT from the amine during deprotection EVEN at room temperature. Our view is that the DMT-amino-modifier C6 is too labile for routine use but it could prove to be useful in situations requiring very mild removal of the amine protecting group. 1.3. The New Amino-Modifier Phosphoramidite One way around these problems is to use a modified trityl with controlled pKR+, where pK R+ is defined by the following formulae: R+ + H2O = ROH + H+ KR+ = ([ROH][H+])/([H2O][R+]) pKR+ = -log KR+ 4,4′-Dimethoxy-4”-thiomethoxytrityl (DMS(O)MT; sulfoxy-form) cation is more stabilized than MMT+, and so the DMS(O)MTprotected amino group is easier to deprotect compared to the MMT-protected one, as shown in Figure 1 on Page 6.135-16-0 supplier The sulfoxy derivative survives conditions of oligonucleotide synthesis and can either be cleaved with standard deblock solution, or left intact for an HPLC purification.PMID:29630205 At the same time, the DMS(O)MT group is fully compatible with cartridge purification. When detritylation on a cartridge is carried out, the DMS(O)MT+, which is more stable than MMT+, does not reattach itself to an amine. The new aminolink phosphoramidite reagent, 5′-DMS(O)MT-Amino-Modifier C6, utilizing this new trityl based protecting group is shown in Figure 5 (1) on Page 8. The reagent is stable in solution in acetonitrile
UV quantification for release of the new protecting group is possible. Extinction coefficients (L/(mol x cm), shown in Figure 1 on Page 6, were measured in 2% TFA/ DCM. In PolyPak detritylation experiments followed.MedChemExpress (MCE) offers a wide range of high-quality research chemicals and biochemicals (novel life-science reagents, reference compounds and natural compounds) for scientific use. We have professionally experienced and friendly staff to meet your needs. We are a competent and trustworthy partner for your research and scientific projects.Related websites: https://www.medchemexpress.com
