Atomic force microscopy and voltammetric characterisation of synthetic homo-oligodeoxynucleotides

Abstract

The controlled bottom-up self-assembling of nucleic acid nanostructures, starting with custom synthetic oligodeoxynucleotides (ODNs) is a current concern in nanotechnology and DNA biosensor technology. The folding properties of the homo-ODNs d(A)10, d(G)10, d(C)10 and d(T)10 were studied using atomic force microscopy (AFM) and voltammetry at carbon electrodes. Network films with knobby appearance were observed for d(A)10, d(C)10 and d(T)10 in AFM, due to the aggregation and coiling of the single-strands under physiological pH. In mild acid pH solutions, d(A)10 double-helical conformations were observed by AFM as network films with lower surface coverage, and detected by voltammetry by the occurrence of the adenine oxidation peak current decrease, whereas d(C)10 forms i-motifs, observed by AFM as spherical aggregates. In Na+ ions containing solutions and for long incubation times, d(G)10 forms G-quadruplexes observed by AFM as spherical aggregates, and detected by voltammetry by the guanine oxidation peak current decrease and the G-quartets oxidation peak occurrence, increase and shift to more positive potentials in a time dependent manner. Long G-nanowires were only formed for increased d(G)10 concentrations, demonstrating the potential of G-rich DNA sequences as a scaffold for nanotechnology applications.