DNA based multi-copper ions assembly using combined pyrazole and salen ligandosides

Abstract

The DNA structure is an ideal building block for the construction of functional nano-objects. In this direction, metal coordinating base pairs (ligandosides) are an appealing tool for the future specific functionalization of such nano-objects. We present here a study, in which we combine the metal ion coordinating pyrazole ligandoside with the interstrand crosslinking salen ligandoside system. We show that both ligandosides, when combined, are able to create stable multi-copper ion complexing DNA double helix structures in a cooperative fashion.

Fig. 1. Depiction of (a) the reversible salen (S) self-base pair; (b) the pyrazole (Pz) self base pair. R = deoxyribose.

Fig. 2. Melting temperatures of duplexes 0a/0b and 1a/1b at different pH values. Conditions: 150 mM NaCl, 10 mM Na₂HPO₄/NaH₂PO₄ buffer pH 6.0/7.4 or CHES buffer pH 9.0, 1 μM oligonucleotide, with or without 1 μM Cu²⁺, final volume of 200 μL.

Fig. 3. Melting temperatures of 1a combined with different counter strands having A, G, C, T or Pz as the counter base. Conditions: 150 mM NaCl, 10 mM CHES buffer pH 9.0, 1 μM oligonucleotide, with or without 1 μM Cu²⁺, final volume of 200 μL.

Fig. 4. Schematic depiction of the investigated duplex 3a/3b and Cu²⁺ titration melting profiles of duplex 3a/3b (Pz = Pyrazole). Conditions: 150 mM NaCl, 10 mM CHES buffer pH 9.0, 1 μM oligonucleotide, final volume of 200 μL.

Fig. 5. (a) Schematic depiction of the assembly of 10 Cu²⁺ pyrazole ligandosides inside a DNA duplex 4a/4b; (b) CD spectral changes of the duplex 4a/4b at various concentrations of Cu²⁺ (from 0 to 15 eq., step of 1 eq.), spectra of 0 eq. and 10 eq. are showed in red. Inset: plot of circular dichroic changes at 300 nm against the ratio of [Cu²⁺]/[4a/4b]. Conditions: 150 mM NaCl, 10 mM CHES buffer pH 9.0, 1 μM oligonucleotide, final volume of 200 μL.

Fig. 6. (a) Overlaid UV spectrum obtained at different concentrations of Cu²⁺ (from 0 to 4 eq.) of the duplex 5a/5b and (b) plot of UV absorbance at 360 nm against the ration of [Cu²⁺]/[5a/5b]; (c) overlaid UV spectrum at different concentrations of Cu²⁺ (from 0 to 4 eq.) of the duplex 6a/6b and (d) plot of UV absorbance at 360 nm against the ration of [Cu²⁺]/[6a/6b]. Conditions: 150 mM NaCl, 10 mM CHES buffer pH 9.0, 3 μM oligonucleotide, 30 eq. ethylenediamine, final volume of 200 μL.

Fig. 7. ESI-Mass spectrum and comparison of experimental data with calculated molecular weights of duplex 6a/6b with 2 eq. Cu²⁺, molecular formula C₃₁₆H₃₈₄O₁₇₆N₉₆P₂₈Cu₂. Peaks contain 10 charges (top) compared with calculation (bottom). Conditions: 150 mM NH₄OAc, 30 μM oligonucleotide, 30 eq. ethylenediamine.

Fig. 8. Schematic depiction of the investigated duplex, S = salen, X = pyrazole. (a) Overlaid CD spectrum at different concentrations of Cu²⁺ (from 0 to 10 eq.) of the duplex 7a/7b; (b) plot of circular dichroic changes at 250 nm against the ration of [Cu²⁺]/[7a/7b]; (c) overlaid UV spectrum under the same conditions as in (a); (d) plot of UV absorbance at 405 nm against the ration of [Cu²⁺]/[7a/7b]. Conditions: 150 mM NaCl, 10 mM CHES buffer pH 9.0, 3 μM oligonucleotide, 30 eq. ethylenediamine, final volume of 200 μL.