Exploiting DNA surfaces for sensing and nanomaterial applications

Abstract

The synthetic methodology for the on-column specific conversion of guanosine to thioguanosine is described, without the use of expensive thioguanosine phosphoramidites. The thiolated oligomer, once self-annealed, exhibits destabilisation compared to the fully complementary duplex as observed in a reduced Tm. Subsequent Cd2+ addition to the disrupted thioG central region indicates a binding ratio of 4:1 thiobase:metal resulting in increased base stacking and overall duplex stability. Equilibrium molecular dynamic calculations reinforce the hypothesis of metal induced restoration of the damaged duplex by the ten-fold reduction in base flexibility upon the addition of the metal stimuli. Hence, the healing of an unstable modified duplex in response to a chemical stimulus has been demonstrated. The electronic behaviour ferrocene modified DNA silicon junctions was investigated by JV curves obtained by using a top eutectic gallium-indium electrode (EGaIn). The charge transport mechanism in single stranded DNA was found to be tunneling with little rectification. However, in double stranded DNA, charge hopping was observed in addition to electron tunneling, with increased rectification. The difference in charge transport between single and double stranded DNA shows promise for the electronic detection of complementary DNA strands in sensing applications and a better understanding of the electronic properties of DNA. Finally, an enhancement in surface immobilised repeat sequences was explored using an enzymatic extension protocol. The oligo seed immobilised on the surface is multiplexed in the z direction increasing the number of repeat sequences per probe molecule. An increase in fluorescence intensity is observed from the oligo seed to the extended DNA following the addition of the fluorescent intercalator PicoGreen. The technique was applied to the BAT-25 micro satellite sequence in which a single base mismatch was distinguished from the fully complementary target. This approach allows increased sensitivity to DNA targets whilst maintaining high selectivity.