Aptamer-Functionalized Platform for Selective Bacterial Isolation and Rapid RNA Purification Using Capture Pins

Efficient bacterial lysis and RNA purification are essential for molecular diagnostics and biosensing applications. This study presents a piezoelectric platform integrated with gold-plated RNA capture pins (RCPs) functionalized with synthetic oligonucleotides to extract and enrich <i>E. coli</i> 16S ribosomal RNA (rRNA). The 3D-printed device enables selective bacterial capture using <i>E. coli</i>-specific aptamers and incorporates a piezoelectric transducer operating at 60 kHz to facilitate bacterial cell wall disruption. The platform demonstrated high specificity for <i>E. coli</i> over <i>B. cereus</i>, confirming aptamer selectivity. <i>E. coli</i> viability assessment demonstrated that positioning the piezoelectric plate in contact with the bacterial suspension significantly improved the bacterial lysis, reducing viability to 33.68% after 15 min. RNA quantification confirmed an increase in total RNA released by lysed <i>E. coli</i>, resulting in 10,913 ng after 15 min, compared to 4310 ng obtained via conventional sonication. RCP-extracted RNA has a threefold enrichment of 16S rRNA relative to 23S rRNA. RT-qPCR analysis indicated that the RCPs recovered, on average, 2.3 ng of 16S RNA per RCP from bacterial suspensions and 0.1 ng from aptamer-functionalized surfaces. This integrated system offers a rapid, selective, and label-free approach for bacterial lysis, RNA extraction, and enrichment for specific types of RNA with potential applications in clinical diagnostics and microbial biosensing.