The sequence of isomeric dinucleotides, bearing 5′ or 3′-terminal phosphate groups, is not correlated to the proton affinity of the nucleobases

The sequence of isomeric dinucleotides, bearing 5'or 3'-terminal phosphate groups, which is not correlated to the proton affinity of the nucleobases, is discussed. The structural determination of dinucleotides by mass spectrometry (MS) follows a simple rule that involves the fragmentation of the parent ion [M-H]- in a MS/MS experiment. The [M-H]- parent ion possess a zwitterionic structure in which the negative charge is placed on a phosphate group. The low energy collisions on the [M-H]- precursor ions indicate that internucleotidic bond dissociation is directed by the position of the terminal group.