Development of a Paper-based Analytical Chip for the Detection of Bacterial 16S rRNA in Wastewater Samples

Analysis of bacteria in the sewage wastewater treatment process is essential for process stabilization and upgrading. Although bacteria are currently being analyzed by molecular biology techniques targeting the 16S rRNA gene, there is a problem that they are time-consuming and labor-intensive. In this study, we developed a paper-based analytical chip by using two types of DNA molecules that specifically bind to bacterial 16S rRNA. We optimized the fabrication method of the detection probe and the paper-based analytical chip, and then detected synthetic DNA having a nucleotide sequence that hybridizes with the designed DNA molecules and bacterial 16S rRNA extracted from an activated sludge sample. We evaluated the amount of nucleic acids quantitatively by taking images of the detection line on the paper-based analytical chip with a smartphone and analyzing its brightness with an open-source image processing program, ImageJ. Our method was able to detect 85 nM of bacterial 16S rRNA concentration in the extract. Nucleic acids that did not hybridize with either of the designed DNA molecules were not detected, demonstrating high selectivity of our method.