Investigation of the Cu binding site at [dCdG] and [CG] base pairs in the absence of a DNA backbone

► Binding sites of Cu2+ are investigated in the [Cu(CG)]+1, [Cu(CG-H)]+1, and [Cu(dCdG)]+1. ► Interstrand complex structures (base-Cu2+-base) are chosen to analyze the MS/MS spectra. ► Linear geometry (CN3-Cu-GN7) is proposed for the [Cu(CG)]+1 complex structure. ► Square planar geometry (CO2CN3-Cu2+-GN7GO6) is proposed for the [Cu(CG-H)]+1.