Numerical Study of Nanoparticle-Enhanced PCR

The polymerase chain reaction (PCR) exponentially amplifies a DNA template and produces large numbers of specific DNA fragments. Because of its high sensitivity and efficiency, it becomes a common technique that is widely used in molecular biological. The addition of nano-gold particles into the template solution was found to greatly enhance the efficacy of PCR [1, 2]. Although the thermal effect has been suggested, the underlying mechanisms are still not clear, e.g. how the temperature field affects the replication of DNA at the molecular level. A typical PCR process consists of repeated cycling of three major steps: (1) fast heating to a temperature around 94°C for separating of the two strands DNA templates into single strand (Denaturation); (2) lowering the temperature to about 54°C for the primers to find the complementary part and anneal to the single stranded templates (Annealing); (3) increase of the temperature again to around 72°C for copying of the single templates with the action of the polymerase enzyme (Extension). The thermal history of the PCR determines the activity of the polymerase and rate of each reaction taken place during the process. And the motion of the primers, the DNA templates and the bases owing to both the Brownian effects and concentration gradients can also influence the specificity and reaction rates. The addition of nano-gold particles is expected to greatly alter both the heat and mass transfer efficiency. Thus, the micro-heat and mass transfer analysis of the nano-gold added PCR process has been performed. The temporal and spatial temperature distribution, and the reactants and products concentration have been numerically simulated. The influence of added nano-gold particles on the polymerase reaction rate, the efficiency and specificity of the PCR has evaluated. The possible thermal wave and resonance of the two-phase fluid at the micro-scale level has also been investigated, as well as the enhanced mass transfer of the templates and the reaction rate. The results show that both the thermal effects and physical properties of the nano-particles have contributed to the increase of the efficiency and specificity in the PCR process.