[en] Polymerase chain reaction (PCR) is an important diagnosis tool in molecular biology, which have been greatly improved by PCR. However, optimizing the experimental conditions is still a problem for PRC. Computer biology can be a solution to this problem. In this paper, developments of the mathematical models for PCA are reviewed. It is believed that this kind of research efforts shall be helpful for optimizing the experimental conditions and providing guidance for the biologists and understanding the mechanism of PCR. (authors)

[en] Nanoparticle PCR (NP-PCR) is a new method to optimize PCR amplification. Suitable amount of Au nanoparticles can improve specificity, sensitivity and extension rate of PCR. In this paper, we compare efficiency of purifying NP-PCR products with different methods. In addition, topographies of DNA products in NP-PCR were observed with atomic force microscope (AFM). The results show that most of DNA products purified directly by routing method remain almost free due to less effect of nanoparticales. The yields decrease when the AuNPs were removed by high-speed centrifugation. A little amount of DNA subsided with AuNPs. (authors)

[en] Fluorescence enhancement in a DNA-dye system is favorable for sensitive and accurate DNA detection/ sensing technologies. In this paper, we report that the fluorescence of the double-stranded DNA (dsDNA) and SYBR Green I (SG) system (dsDNA-SG) can be effectively enhanced by negatively charged magnetic iron oxide (Fe_2O_3@DMSA) and gold nanoparticles in suitable concentrations, but positively charged nanoparticles quench the fluorescence. Effects of the Fe_2O_3@DMSA on the fluorescence intensities are investigated with dsDNA-SG of different lengths or complexities. The results show that nanoparticles perform similarly in enhancing fluorescence intensity for several kinds of dsDNA. However, the dsDNA concentration determines the fluorescence amplitude. It shows that fluorescence intensity of lower concentration dsDNA is enhanced remarkably in DNA-SG. The finding may be useful in sensitive biomolecular detection. (authors)

[en] A mathematical model of polymerase chain reaction (PCR) containing uncertain and time-varying parameters has become important for model-based guidance experiment design. In this study, the local and global sensitivity analyses were conducted to identify that the responses of PCR process vary with their parameters of initial reactant concentrations and rate constants. Our results showed that the template concentration in initial reactant concentrations had the largest effect on DNA amplification yield. The rate constant characteristics showed that the local sensitivity basically determined the specific reactions; and the global sensitivity, the non-specific reactions. Our work should be helpful for optimizing PCR experimental conditions, and determining the PCR parameter sensitivities. (authors)

[en] Gold nanoparticles (AuNPs) have been proven to be able to improve the specificity or increase the efficiency of a polymerase chain reaction (PCR) when a suitable amount of AuNPs was used. However, there is still a lack of systematic evaluation of AuNPs in real-time PCR. In this study, DNA degradation and the fluorescence quenching effect of AuNPs were first tested in real-time PCR. Then two different kinds of Taq DNA polymerase, native and recombinant Taq polymerase, were employed to evaluate the AuNPs' effect on the threshold cycle (C_T) values, standard curves and melting curves in real-time PCR. Different ratios of the amount of native Taq DNA polymerase to the amount of AuNPs were also tested. It was found that AuNPs could be applied in real-time PCR with correlation coefficient R²>0.989. The combination of 2.09 nM AuNPs with 3.75 U of native Taq DNA polymerase could make the amplification curves shift to the left and enhance the efficiency of the real-time PCR (0.628 39 without AuNPs compared with 0.717 89 with 2.09 nM AuNPs), thus enabling faster detection in comparison with those of control samples. However, no improvement ability of AuNPs was found in real-time PCR based on recombinant rTaq DNA polymerase. Besides, the results suggest that a complex interaction exists between AuNPs and native Taq DNA polymerase