At present, automated next-generation sequencing (NGS) library preparation workflows predominantly rely on super-paramagnetic beads and plate-based magnets for sample cleanup and fragment size-selection. A typical bead-based cleanup method requires six pipette tips per sample, a labware transport mechanism, and fine-tuning of pipetting heights to ensure complete supernatant removal from pelleted beads. DPX Technologies’ NiXTips contain immobilized silica media within robotic pipette tips and offer an automated bead-free alternative for cleanup and size-selection. The NiXTip workflow requires only two pipette tips per sample and five fewer deck positions than bead-based methods. In this study, we compared the performance of NiXTips against beads in two NGS library preparation workflows, including downstream sequencing analysis. In all areas, NiXTips had equivalent or superior performance compared to beads, demonstrating the suitability of using NiXTips for NGS library preparation workflows.

DNA recovery using NiXTips (DPX Technologies, NIX-HM300-96) was evaluated on a Hamilton VANTAGE liquid handler (Figure 1). A 1 kb Plus DNA ladder (Thermo, SM0311) diluted to 20 ng/µL (1 µg total input; n = 6 per condition) was used as the input sample. Samples were mixed with binding buffer (DPX, NIXBB-001) at a 1:1 buffer-to-sample ratio and subjected to 5, 10, 20, or 30 NiXTips binding cycles. Tips were washed using two 100 µL aspirate/dispense cycles with 80% ethanol, then dried by four air-dry cycles consisting of a 1000 µL air gap blown through the silica media (Table 1). DNA was eluted in 50 µL PCR-grade water at room temperature, and eluates were quanti ed using the Qubit BR dsDNA assay (Invitrogen, Q32853).

Table 1.

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