Glen Report 34-14: New Product — Ac-dC-5’-CE Phosphoramidite

In recent years, the need for 5’-3’ direction synthesis reagents has increased significantly. Whether researchers are looking for enhanced nuclease resistance, trying to incorporate a special modification like a dideoxynucleotide or simply needing to synthesize oligonucleotides on a surface that can be subsequently extended with polymerases,1, 2 they are constantly looking for a wider variety of reverse synthesis reagents that give them more options to accomplish what they need. One option that users of our DNA reverse synthesis reagents do not have is AMA deprotection. 

Our traditional offering of dC has been a benzoyl-protected one, which, like all other benzoyl-dC protected phosphoramidites, is incompatible with any deprotection method that involves methylamine. Instead of cleaving the benzoyl group off of dC, the methylamine can instead displace benzamide to give N4-methyl-dC.3 In the case of AMA deprotection, this undesired conversion is 5-10 %. In the case of gaseous methylamine deprotection, it can be much more. 

Figure 1
Figure 1. Ac-dC-5’-CE Phosphoramidite

To give our customers the option of using methylamine for deprotection, we are now offering reverse Ac-dC phosphoramidite as well (Figure 1). It can be used in exactly the same way as the reverse Bz-dC phosphoramidite. For both coupling and deprotection, no changes are needed from standard methods recommended by the synthesizer manufacturer.

References

  1. The Glen Report, 1993, 6.1, 6.
  2. The Glen Report, 2019, 31.1, 11-12.
  3. The Glen Report, 2014, 26.1, 4-6.

Product Information

dC-5’-CE Phosphoramidite 

Ac-dC-5’-CE Phosphoramidite