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Background  Mechlorethamine [ClCH 2 CH 2 N(CH 3 )CH 2 CH 2 Cl], a nitrogen mustard alkylating agent, has been proven to form a DNA interstrand crosslink at a cytosine-cytosine (C-C) mismatch pair using gel electrophoresis. However, the atomic connectivity of this unusual crosslink is unknown.    Methodology/Principal Findings  HPLC-UV, MALDI-TOF-MS, and ESI-MS/MS were used to determine the atomic connectivity of the DNA C-C crosslink formed by mechlorethamine, MALDI-TOF-MS of the HPLC-purified reaction product of mechlorethamine with the DNA duplex d[ CTCACAC C GTGGTTC ]•d[ GAACCAC C GTGTGAG ] (underlined bases are a C-C mismatch pair) indicated formation of an interstrand crosslink at m/z 9222.088 [M−2H+Na] + . Following enzymatic digestion of the crosslinked duplex by snake venom phosphodiesterase and calf intestinal phosphatase, ESI-MS/MS indicated the presence of dC-mech-dC [mech = CH 2 CH 2 N(CH 3 )CH 2 CH 2 ] at m/z 269.2 [M] 2+  (expected m/z 269.6, exact mass 539.27) and its hydrolytic product dC-mech-OH at m/z 329.6 [M] +  (expected m/z 329.2). Fragmentation of dC-mech-dC gave product ions at m/z 294.3 and 236.9 [M] + , which are both due to loss of the 4-amino group of cytosine (as ammonia), in addition to dC and dC+HN(CH 3 )CH = CH 2 , respectively. The presence of m/z 269.2 [M] 2+  and loss of ammonia exclude crosslink formation at cytosine N 4  or O 2  and indicate crosslinking through cytosine N 3  with formation of two quaternary ammonium ions.    Conclusions  Our results provide an important addition to the literature, as the first example of the use of HPLC and MS for analysis of a DNA adduct at the N 3  position of cytosine.

HPLC-UV, MALDI-TOF-MS and ESI-MS/MS Analysis of the Mechlorethamine DNA Crosslink at a Cytosine-Cytosine Mismatch Pair