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

Abstract

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 E. coli 16S ribosomal RNA (rRNA). The 3D-printed device enables selective bacterial capture using E. coli-specific aptamers and incorporates a piezoelectric transducer operating at 60 kHz to facilitate bacterial cell wall disruption. The platform demonstrated high specificity for E. coli over B. cereus, confirming aptamer selectivity. E. coli 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 E. coli, 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.