We report on a novel DNA affinity biosensor which utilises the capture of a neutral charged single stranded (ss) morpholino DNA on a gold electrode to trigger an electrostatic repulsion of negatively charged silicotungstate anions and, in turn, enabled detection of the hybridisation of complementary base pairs. The repulsion of the anions, as a redox indicator, is reflected by a decrease in its electrochemical response with increasing target ss-DNA concentration. A theoretical framework for DNA detection by the affinity biosensor is proposed and verified by electrochemical measurements in the presence of the target ss-DNA by either dc cyclic voltammetry or Fourier transformed alternating current voltammetry (FTACV). The optimised conditions for the capture of the target ss-DNA and the electrochemical detection include 1 μM thiolated neutral morpholino oligo-nucleotide probe, hybridisation time of 10 min, 0.25 mM [α-SiW 12 O 40 ] 4- , and 25 mM phosphate buffer. In addition, the use of the 5th harmonic component of the FTACV gave the most sensitive response for the detection of the target ss-DNA. Under these conditions, the DNA affinity biosensor, based on FTACV detection, achieved a minimum detectable concentration of 0.1 pM ss-DNA and a linear concentration range of 0.1–1000 pM. The biosensor also successfully distinguished between some matched and mismatched base pairs.