Cleaning Grease-Contaminated Tips for PCR Applications: Why Surfactant Choice Matters

Q: We need to clean grease from pipette tips and other labware used in PCR workflows. We’re concerned about detergent residues interfering with our results. What do you recommend?

A: This is a genuinely important question in molecular biology labs, and the answer comes down to surfactant chemistry. Anionic surfactants — the kind found in many common lab detergents including Alconox® Powdered Precision Cleaner and Liquinox® Critical Cleaning Liquid Detergent— are well-documented inhibitors of PCR. Compounds like dodecyl sulfate and alkylbenzene sulfonates can denature or interfere with the polymerase enzyme, even at trace levels. So if you’re cleaning labware that will be used in PCR, the surfactant chemistry of your detergent matters as much as the cleaning performance.

The practical solution is to use a nonionic detergent. Nonionic surfactants do not carry the same risk of enzyme inhibition, making them a much safer choice for PCR-sensitive applications. For cleaning grease from pipette tips and similar labware in an ultrasonic cleaner, we recommend Alcojet® Low Foaming Powdered Detergent at a 1% concentration (10 g/L) in warm to hot water. Alcojet is nonionic, low-foaming, and well-suited for ultrasonic cleaning — the mechanical action of the ultrasonic bath, combined with Alcojet’s surfactant system, does an excellent job of lifting and removing greasy residues from tight geometries like tip interiors and connectors. Follow with a thorough water rinse.

A natural question to ask is: why should it matter if all Alconox, LLC detergents are free rinsing, even the ones with anionic surfactants?

Important to note that in automated equipment, rinsing may not be to the levels required to remove all trace amounts of PCR interfering anionic surfactant. While even nonionic surfactants should be thoroughly rinsed away before PCR use, and could be a source of downstream assay interference, it is of course a notably larger issue when it is an anionic surfactant.

Do you have a critical cleaning question for the experts at Alconox, LLC?  Search TechNotes to see if it’s been answered before or Ask Alconox.

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