posted on 2019-08-20, 18:33authored bySoheil Pourshahian, Sergei M. Gryaznov
Hydrolysis
of N3′-P5′ phosphoramidate and thiophosphoramidate
oligonucleotides with 0.1% formic acid leads to the cleavage of the
3′ N–P bond and generates two products, one of which
contains a 5′-phosphate. Analysis of the hydrolytic products
by liquid chromatography, coupled with mass spectrometry, reveals
the mass ladder from both termini, which is used to determine the
sequence. While acid hydrolysis does not result in depurination, internal
fragments especially in the low mass range are detected. The method
is applied to DNA and RNA analogues with and without modifications
at the 2′-position. This approach enables rapid sequence confirmation
of synthetic phosphoramidate oligonucleotides for quality control
as well as denovo sequencing.