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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 34, Number 4
BKCSDE 34(4)
April 20, 2013 

Structural Analysis of Cu Binding Site in [Cu(I)·d(CpG)·d(CpG)−2H]−1 Complex
Yu-Jin Im, Sang-Mi Jung, Ye-Song Kang, Ho-Tae Kim*
d(CpG), d(CpG)·d(CpG) dinucleotide duplex, [Cu(I)·d(CpG)·d(CpG) − 2H]−1 complex, Mass spectrometry (MS), MS/MS
The Cu cation binding sites of [Cu(I)·d(CpG)·d(CpG) – 2H]−1 complex have been investigated to explain the [Cu·DNA] biological activity caused by the Cu association to DNA. The structure of [Cu(I)·d(CpG)·d(CpG) – 2H]−1 complex was investigated by electrospray ionization mass spectrometry (ESI-MS). The fragmentation patterns of [Cu(I)·d(CpG)·d(CpG) – 2H]−1 complex were analyzed by MS/MS spectra. In the MS/MS spectra of [Cu(I)·d(CpG)·d(CpG) – 2H]−1 complex, three fragment ions were observed with the loss of d(CpG), {d(CpG) + Cyt}, and {d(CpG) + Cyt + dR}. The Cu cation binds to d(CpG) mainly by substituting the H+ of phosphate group. Simultaneously, the Cu cation prefers to bind to a guanine base rather than a cytosine base. Five possible geometries were considered in the attempt to optimize the [Cu(I)·d(CpG)·d(CpG) – 2H]−1 complex structure. The ab initio calculations were performed at B3LYP/6-31G(d) level.
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