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...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.展开更多
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 GreenⅠ...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 GreenⅠ(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.展开更多
Nanoparticle PCR is a novel method to optimize DNA amplification. It performs well in improving specificity, enhancing sensitivity and speed. Several mechanisms were proposed in previous studies: one was based on the ...Nanoparticle PCR is a novel method to optimize DNA amplification. It performs well in improving specificity, enhancing sensitivity and speed. Several mechanisms were proposed in previous studies: one was based on the interaction between gold nanoparticles (AuNPs) and DNA while the other was attributed to the heat transfer property of AuNPs. In this paper, we propose that the interaction between AuNPs and DNA polymerase can significantly influence PCR. First, the addition of DNA polymerase can eliminate the inhibitory effects of excess AuNPs. Second, the addition of AuNPs will increase yield of the desired PCR product and make the optimum concentration of DNA polymerase move to higher value. Third, while excess polymerase might inhibit amplification efficiency, AuNPs can reverse this process and the yield of PCR amplification. Based on these results we propose a possible mechanism that AuNPs might modulate the activity of polymerase and improve PCR amplification.展开更多
基金Supported by the Shanghai Municipal Commission for Science and Technology (09395811700)National Basic Research Program of China (2007CB936000)
文摘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.
基金supported by grants from the National Science Foundation of China (No.10975175,90923002)the Chinese Academy of Sciences(No.KJCX2-EW-N03)
文摘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 GreenⅠ(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.
基金Supported by the National Natural Science Foundation of China (Grant Nos. 10335070, 60537030, and 20404016)the Major State Research Development Pro-gram of China (Grant No. 2006CB933000)+1 种基金Shanghai Municipal Commission for Science and Technology (Grant No. 0652NM006)the Chinese Academy of Sci-ences
文摘Nanoparticle PCR is a novel method to optimize DNA amplification. It performs well in improving specificity, enhancing sensitivity and speed. Several mechanisms were proposed in previous studies: one was based on the interaction between gold nanoparticles (AuNPs) and DNA while the other was attributed to the heat transfer property of AuNPs. In this paper, we propose that the interaction between AuNPs and DNA polymerase can significantly influence PCR. First, the addition of DNA polymerase can eliminate the inhibitory effects of excess AuNPs. Second, the addition of AuNPs will increase yield of the desired PCR product and make the optimum concentration of DNA polymerase move to higher value. Third, while excess polymerase might inhibit amplification efficiency, AuNPs can reverse this process and the yield of PCR amplification. Based on these results we propose a possible mechanism that AuNPs might modulate the activity of polymerase and improve PCR amplification.
