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

  • Im, Yu-Jin ;
  • Jung, Sang-Mi ;
  • Kang, Ye-Song ;
  • Kim, Ho-Tae
  • Received : 2013.03.27
  • Accepted : 2013.03.28
  • Published : 2013.04.20

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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Acknowledgement

Supported by : Kumoh National Institute of Technology