Location and base selectivity on fragmentation of brominated oligodeoxynucleotides

Bromine‐modified oligodeoxynucleotides (ODNs) were fragmented in the electrospray source to study the influence of brominated bases on fragmentation. Several 13‐mer ODNs containing a brominated pyrimidine base, BrdU (5‐bromodeoxyuridine) or BrdC (5‐bromodeoxycytidine), were analyzed. Low cone voltage fragmentation yields a loss of the brominated base with a preferential loss for the brominated base closer to the 5′‐end (2‐position > 4‐position > 12‐position) as well as a preferential loss of BrdU over BrdC. Higher cone voltage produces backbone fragmentation with complementary a n ‐base and w m ions close to the brominated base. On the basis of these observations, we located the brominated base in the sequence for all of the ODNs studied. Copyright © 2005 John Wiley & Sons, Ltd.