Oligonucleotide sequencing using guanine-specific methylation and electrospray ionization ion trap mass spectrometry

This paper describes a novel method to map guanine bases in short oligonucl eotides using a simple chemical modification reaction and subsequent analys is by electrospray ionization ion trap mass spectrometry (ITMS). In situ gu anine-specific methylation followed by gas-phase fragmentation permits the determination of the positions of all guanine residues, Collision-induced d issociation (CID) of the monomethylated oligonucleotide strand promotes rap id depurination and further collision (MS3) of the apurinic oligonucleotide leads to preferential cleavage of the backbone at the site of depurination , The mass of the resulting complementary product ions verifies the positio n of each guanine base in the sequence, The utility of this methodology is demonstrated for oligonucleotide sequences up to 10 bases in length. In add ition, this technique successfully illustrates the use of selective fragmen tation for sequencing oligonucleotides by ITMS. Copyright (C) 1999 John Wil ey & Sons, Ltd.