Computer modeling to optimize the sensitivity of an optical DNA nanosensor

Abstract

This paper describes how the sensitivity of an optical DNA nanosensor based on MNPs and QDs was enhanced by using computer simulations including an innovative software, Grasshopper. The data used was derived from a previously constructed mechanism which, although successful in detecting target DNA qualitatively, raised some areas for further investigation. By adjusting the relative proportions of DNA probes, MNPs and QDs in the model, we were able to simulate a range of different reactions in the sensor and to measure them quantitatively. We were able to observe MNPs and QDs binding to more than one strand of DNA and to better understand how they network in different concentrations of the solution. We found a direct correlation coefficient of 0.9666 between the fluorescent intensity of the CdSe/ZnS QDs and the concentration of tDNA within the range of 1 × 10-6-3.9 × 10-9 M. To optimize the sensor further, we also modified the hybridization procedure, breaking it into two steps. This produced a very satisfactory LOD calculation of 1.75 × 10-9 M. Finally, when we applied the 2 step hybridization procedure we were able to improve the sensitivity of the optical nanosensor up to 20% furthur.