Gold Nanoparticle Effects in Polymerase Chain Reaction: Favoring of Smaller Products by Polymerase Adsorption

Gold nanoparticles were recently reported to reduce the formation of nonspecific products in polymerase chain reaction (PCR) at remarkably low temperatures, with hypothesized mechanisms including adsorption of DNA and heat-transfer enhancement. In contrast to these reports, we report that gold nanoparticles do not enhance the specificity of PCR but rather suppress the amplification of longer products while favoring amplification of shorter products, independent of specificity. Gold nanoparticles bearing a self-assembled monolayer of hexadecanethiol did not affect PCR, suggesting that surface interactions play an essential role. This role was further confirmed by experiments in which a similar effect on PCR was observed for the same total surface area of particles over a 100-fold range of per-particle surface area. The effect was seen with Taq and Tfl polymerases but not with Vent polymerase, and the effects of nanoparticles can be reversed by increasing the polymerase concentration or by adding bovine serum albumin (BSA). Transient high-temperature nanoparticle pre-exposure of PCR mix containing polymerase but not template or primers, followed by nanoparticle removal, modified subsequent nanoparticle-free PCR. Interaction between polymerase and gold nanoparticles was confirmed by changes in nanoparticle absorption spectrum and electrophoretic mobility in the presence of polymerase. Taken together, these results suggest that the nanoparticles nonspecifically adsorb polymerase, thus effectively reducing polymerase concentration

A plot of the optimized squareness value, <i>n</i>, vs etch time.

<p>A plot of the optimized squareness value, <i>n</i>, vs etch time.</p

SEM image of a 75nm wide square pattern fabricated by SLIM processing of a dot array with 100nm pitch.

<p>SEM image of a 75nm wide square pattern fabricated by SLIM processing of a dot array with 100nm pitch.</p

The SEM images compares a) a SLIM processed pattern and b) the same sample after heat treatment for one hour at 400 °C.

<p>The SEM images compares a) a SLIM processed pattern and b) the same sample after heat treatment for one hour at 400 °C.</p

A plot of pattern size vs etch time for different precursor openings showing little change in the pattern size distribution.

<p>A plot of pattern size vs etch time for different precursor openings showing little change in the pattern size distribution.</p

Nickel was electrodeposited into a SLIM pattern with 80nm square opening.

<p>The SEM images show a) a 52 degree projection of the nickel pillars after removing the resist and (b) a 52 degree projection of the same sample after argon plasma treatment.</p

A plot showing the influence of SLIM process time and precursor thickness on the pattern width.

<p>Each curve approaches an asymptote at approximately 183nm revealing the self-limiting etch process.</p

Diagram describing the SLIM process.

<p>The precursor is dot patterns separated by a wall of thickness a₀ and b₀. SLIM processing narrows both walls at the same rate to a thickness of a₁ and b₁. At a critical thickness the etch rate reduces significantly resulting in little change towards a₂, but b₂ continues to narrow. As b₂ approaches the critical thickness, the pattern converges to a square.</p

A plot of the measured squareness ratio vs etch time for each precursor.

<p>A plot of the measured squareness ratio vs etch time for each precursor.</p

SEM images of the original precursors (a,c,e) and after SLIM processing (b,d,f).

<p>The diameters of the circles in the precursor are: a) 100nm, c) 137nm and e) 175nm.</p