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Technical Briefs

Numerical Simulation of Au Nanoparticles Effect on the PCR Process

[+] Author and Article Information
Chao Chen, Aili Zhang, Xiaodong Zhang, Jun Hu

Department of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China

Lisa X. Xu1

Department of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200240, P.R. Chinalisaxu@sjtu.edu.cn

1

Corresponding author.

J Biomech Eng 131(7), 074512 (Jun 12, 2009) (7 pages) doi:10.1115/1.3147746 History: Received September 12, 2008; Revised May 03, 2009; Published June 12, 2009

Gold nanoparticles have been found to greatly enhance the polymerase chain reaction (PCR) specificity and yield in recent studies. However, the underlying mechanism is still unclear, though different hypotheses have already been proposed. In this study, a mass-action based model has been developed to investigate the effect of Au nanoparticles on the two-round PCR results. The great affinity of Au nanoparticles to the single-stranded DNA is taken into consideration. Each nanoparticle is treated as a bioreactor and/or a selector, around which, reaction equations are coupled to simulate the particle effect, and to investigate the key parameters that might influence such an effect. It is assumed that there exists a competing mechanism between the specific and nonspecific bindings, both in the solution and on the particle surface during the reactions. The numerical predictions accord well to the experimental results, and can be used to explain the Au nanoparticles’ effect on the enhancement of the PCR specificity and efficiency.

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Copyright © 2009 by American Society of Mechanical Engineers
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Figures

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Figure 1

The 10.28 nm Au nanoparticle is added into the PCR mixture, and for lanes 1–8 its final concentration are 0 nm, 0.07 nm, 0.14 nm, 0.21 nm, 0.28 nm, 0.35 nm, 0.42 nm, and 0.49 nm, respectively; lane M is for the marker in Ref. 3 (with the permission of authors)

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Figure 2

Demonstration of seven lengths of templates and primers in PCR. Equations 1,2,3,4,5,6,7,8 correspond to the reactions in the solution 1,2,3,4,5,6,7,8.

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Figure 3

Schematics of PCR on the Au surface

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Figure 4

Flow chart of all the reactions in PCR modeling with Au nanoparticles. i denotes various kinds of templates as seen in Nomenclature. Equations 1,2,3,4,5,6,7,8 are equations in the Appendix.

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Figure 5

Variation of final yields with specific/nonspecific ratios of binding rate constants

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Figure 6

PCR specific and nonspecific yields with Au concentrations under different rAu, rsol=1

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Figure 7

The predicted yields of various templates types at the optimum Au concentration without and with Au nanoparticles; rsol=1, rAu=3

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Figure 8

PCR specific and nonspecific total yields, yields in the solution and on the Au surface with respect to Au concentration; rsol=1, rAu=3

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Figure 9

The fitted reff and total yield with respect to rAu while rsol=1 at the optimum Au concentration

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