Inhibitory effect of common microfluidic materials on PCR outcome

Abstract

Microfluidic chips have a variety of applications in the biological sciences and medicine. In contrast with traditional experimental approaches, microfluidics entails lower sample and reagent consumption, allows faster reactions and enables efficient separation. Additionally microfluidics offers other advantages accruing from the fluids’ various distinct behaviors, such as energy dissipation, fluidic resistance, laminar flow, and surface tension. Biological molecules suspended in fluid and transported through microfluidics channels interact with the channel-wall material. This interaction is even stronger in high surface-area-to-volume ratio (SAVR) microfluidic channels. Adsorption and inhibition of biomolecules occur when these materials come in contact with biomolecular reaction components. Polymerase chain reaction (PCR) is a thermal cycling procedure for amplifying target DNA. The PCR compatibility of silicon, silicon dioxide (SiO2) and other surfaces have been studied; however the results are inconclusive. Usually for protein-surface interaction measurements, bulky and expensive equipment is used, such as Atomic Force Microscopy (AFM), Scanning or Transmission Electron Microscopy (SEM, TEM), spectrophotometric protein concentration measurement, Fourier transform infrared spectroscopy (FTIR) or X-Ray photoelectron spectroscopy (XPS). The PCR reaction components include the DNA template, primers, DNA polymerase (the main component), dNTPs, a buffer, divalent ions (MgCl2), and KCl. We designed a simple, relatively quick measurement that only requires a PCR cycler; thus it mimics actual conditions in PCR cycling. In our study, we evaluated the inhibitory affect of different materials on PCR, which is one of the most frequently used enzymatic reactions in microfluidics. PCR reaction optimization through choice of surface materials is of the upmost importance, as it enables and improves enzymatic reaction in microfluidics. Our assessment of the PCR compatibility of various materials commonly used while producing microfluidic devices is also pertinent and beneficial to other enzymatic reactions in microfluidic devices. Most PCR-friendly materials exhibit similar signals regardless of the inclusion or not of BSA in the PCR mixture; these materials are PP, PTFE, PDMS, wax (Tm 80°C), SiO2 quartz, pyrex and soda-lime glasses, NOA68, and mineral oil. Our results showed that there was near total adsorption of template DNA when the wax (Tm 60°C) was used (RBI = 9.2×101). In contrast, when NOA61, mineral oil and acrylic glue materials were employed, significant adsorption occurred (RBI < 1.5×103). The polymerase-inhibition experiments indicate that following materials do not have strong effects (RBI > 1.1×103) on polymerase: PC, PP, PTFE, PDMS, silicon with a layer of 560 nm SiO2, SiO2 quartz, pyrex, and soda-lime glass. Slight polymerase inhibition (RBI < 9.2×102) was observed with PMMA, PVC, waxes (Tm 56°C and 80°C), silicon, and NOA68. A very strong or near total inhibition (RBI < 1.8×102) was observed with wax (Tm 60°C), ITO glass, SU-8, NOA61, metal tubes, mineral oil, epoxy, and the acrylic glues. Our results show that material selection for microfluidic PCR chips, which are characterized by large SAVR, is a vital part of optimizing PCR outcome. This study of the inhibitory effect of various common microfluidics materials has provided a new rapid testing method using only a PCR cycler, and it has confirmed and expanded the list of tested materials. The type of PCR compatibility test enables the most effectual choice of materials for use in biology-related experiments.