(1386-C) Tip-Top Cleanup: SPRI Tips for Dynamic PCR Product Cleanup

Abstract: Purification and size selection of PCR products remains a critical step in many next-generation sequencing workflows. Paramagnetic SPRI beads are the gold standard for automating PCR cleanups. However, they present multiple challenges: bead storage at 4°C, ensuring uniform suspension of bead solutions over long periods of time, and logistics of handling large volumes of beads on automated liquid handlers. To address these challenges, we have developed a tip-based cleanup protocol using “SPRI tips,” specifically designed for incorporation into automated workflows.

SPRI tips have been purposefully designed for comparable DNA recovery and size selection to SPRI beads, effectively eliminating the need for magnetic beads or magnetic manipulation. The workflow of a SPRI tip-based cleanup begins with binding the DNA to an internal material housed within the tip, followed by a brief wash step, and finally eluting the target product off the tip material. This new technique uses a binding buffer added to the PCR product that can be adjusted for specific left-handed size selections.

Here we demonstrate that SPRI tip cleanups are comparable to bead-based cleanups in both amount of recovered DNA product and overall cleanup speed. Additionally, the adaptable workflow of tip-based cleanups allows for custom optimization to maximize product recovery or streamline protocol timing. Notably, even the fastest cleanup still ensures a cleaned PCR product. SPRI tip cleanups are easily automated on the Agilent Bravo platform, and the inherent benefits of a tip-based cleanup method would allow for ease of use in high-throughput sample processing.