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http://dx.doi.org/10.5012/bkcs.2013.34.4.1232

Structural Analysis of Cu Binding Site in [Cu(I)·d(CpG)·d(CpG)-2H]-1 Complex  

Im, Yu-Jin (Department of Applied Chemistry, Kumoh National Institute of Technology)
Jung, Sang-Mi (Department of Applied Chemistry, Kumoh National Institute of Technology)
Kang, Ye-Song (Department of Applied Chemistry, Kumoh National Institute of Technology)
Kim, Ho-Tae (Department of Applied Chemistry, Kumoh National Institute of Technology)
Publication Information
Bulletin of the Korean Chemical Society / v.34, no.4, 2013 , pp. 1232-1236 More about this Journal
Abstract
The Cu cation binding sites of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex have been investigated to explain the $[Cu{\cdot}DNA]$ biological activity caused by the Cu association to DNA. The structure of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex was investigated by electrospray ionization mass spectrometry (ESI-MS). The fragmentation patterns of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex were analyzed by MS/MS spectra. In the MS/MS spectra of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ 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 $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex structure. The ab initio calculations were performed at B3LYP/6-31G(d) level.
Keywords
d(CpG); $d(CpG){\cdot}d(CpG)$ dinucleotide duplex; $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex; Mass spectrometry (MS); MS/MS;
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