Imaging immobilised ssDNA and detecting DNA hybridisation by means of the repelling mode of scanning electrochemical microscopy (SECM)

Abstract

The supposed repelling mode of scanning electrochemical microscopy (SECM) allows truly label-free electrochemical recognition of the presence and hybridisation of nucleic acids that are immobilised on conducting DNA chips. Basically, the SECM-based detection of single- and double-stranded DNA profits from the electrostatic repulsion between deprotonated phosphate groups at the backbone of the oligonucleotides and a free-diffusing negatively charged redox mediator (e.g. [Fe(CN) 6] 3−/4−). In electrolytes of proper pH and ionic strength, this coulomb interaction is heavily influencing the diffusion properties of the mediator in the vicinity of the surface-anchored DNA strands. This charge interaction modulates the diffusional mass transport for the charged redox species in the DNA modified regions, and thus locally decreases the positive feedback currents measured with a SECM tip placed within the electrochemical nearfield of the chip surface. This approach was used to study arrays of synthetic 20-base oligonucleotide probes that were immobilised on monolayer-modified gold surfaces. Evidence is provided that the density of probes, the ionic strength of solution and the tip-to-sample distance have a strong impact on the capability of the repelling mode of SECM to visualise probe spots and hybridisation while the concentration of the chosen mediator did not significantly affect detection.