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Keywords:

  • absorption;
  • DNA;
  • density functional calculations;
  • metal;
  • nucleobases

Abstract

Using density functional theory calculations, we investigated the structural, energetic, electronic, and optical properties of recently synthesized duplex DNA containing metal-mediated base pairs. The studied duplex DNA consists of three imidazole (Im) units linked through metal (Im-M-Im, M=metal) and four flanking A:T base pairs (two on each side). We examined the role of artificial base pairing in the presence of two distinctive metal ions, diamagnetic Ag+ and magnetic Cu2+ ions, on the stability of duplex DNA. We found that metal-mediated base pairs form stable duplex DNA by direct metal ion coordination to the Im bases. Our results suggest a higher binding stability of base pairing mediated by Cu2+ ions than by Ag+ ions, which is attributed to a larger extent of orbital hybridization. We furthermore found that DNA modified with Im-Ag+-Im shows the low-energy optical absorption characteristic of π–π*orbital transition of WC A:T base pairs. On the other hand, we found that the low-energy optical absorption peaks for DNA modified with Im-Cu2+-Im originate from spin–spin interactions. Additionally, this complex exhibits weak ferromagnetic coupling between Cu2+ ions and strong spin polarization, which could be used for memory devices. Moreover, analyzing the role of counter ions (Na+) and the presence of explicit water molecules on the structural stability and electronic properties of the DNA duplex modified with Im-Ag+-Im, we found that the impact of these two factors is negligible. Our results are fruitful for understanding the experimental data and suggest a potential route for constructing effective metal-mediated base pairs in duplex DNA for optoelectronic applications.