Nanoparticles Affect PCR Primarily via Surface Interactions with PCR Components: Using Amino-Modified Silica-Coated Magnetic Nanoparticles as a Main Model

Abstract

Nanomaterials have been widely reported to affect the polymerase chain reaction (PCR). However, many studies in which these effects were observed were not comprehensive, and many of the proposed mechanisms have been primarily speculative. In this work, we used amino-modified silica-coated magnetic nanoparticles (ASMNPs, which can be collected very easily using an external magnetic field) as a model and compared them with gold nanoparticles (AuNPs, which have been studied extensively) to reveal the mechanisms by which nanoparticles affect PCR. We found that nanoparticles affect PCR primarily by binding to PCR components: (1) inhibition, (2) specifity, and (3) efficiency and yield of PCR are impacted. (1) Excess nanomaterials inhibit PCR by adsorbing to DNA polymerase, Mg(2+), oligonucleotide primers, or DNA templates. Nanoparticle surface-active groups are particularly important to this effect. (2, a) Nanomaterials do not inhibit nonspecific amplification products caused by false priming as previously surmised. It was shown that relatively low concentrations of nanoparticles inhibited the amplification of long amplicons, and increasing the amount of nanoparticles inhibited the amplification of short amplicons. This concentration phenomenon appears to be the result of the formation of "joints" upon the adsorption of ASMNPs to DNA templates. (b) Nanomaterials are able to inhibit nonspecific amplification products due to incomplete amplification by preferably adsorbing single-stranded incomplete amplification products. (3) Some types of nanomaterials, such as AuNPs, enhance the efficiency and yield of PCR because these types of nanoparticles can adsorb to single-stranded DNA more strongly than to double-stranded DNA. This behavior assists in the rapid and thorough denaturation of double-stranded DNA templates. Therefore, the interaction between the surface of nanoparticles and PCR components is sufficient to explain most of the effects of nanoparticles on PCR.

Enhancement of the polymerase chain reaction by tungsten disulfide

“…Many researchers tried to use nanomaterials as additives to optimize the PCR efficiency. [14][15][16][17][18] Up to now, gold nanoparticles (AuNPs), graphene oxide (GO), quantum dots (QDs), carbon nanotubes (CNTs), and some other metal nanoparticles and nanocomposites have been used to improve the specicity and efficiency of the PCR. [19][20][21][22][23] Although AuNPs can improve the specicity and efficiency of PCR, its own colour limited its application in some colorimetric reactions.…”

The presence of residual gold nanoparticles in samples interferes with the RT-qPCR assay used for gene expression profiling

“…The deliberate addition of ENMs to alter the specificity and efficiency of a PCR reaction has been reported [ 18 , 19 ]. However, if the deliberate addition of an ENM may alter the mechanics of the PCR, then the unintentional intracellular (residual) amount of ENM will also alter the PCR assay.…”

Tessellated permanent magnet circuits for flow-through, open gradient separations of weakly magnetic materials

“…The potential drawback of the method is the reliance on the magnetic labeling reagents that may have an undesirable effect on the target cell biology and may adversely affect downstream cell product processing and molecular analysis for diagnostic applications [3]. In particular, the presence of iron in the analyte is known to interfere with the polymerase chain reaction (PCR) [4]. The issue is even more acute in case of the cell product being intended for therapeutic applications.…”