A microfluidic chip that will not prime correctly is one of the more frustrating problems in a flow experiment, partly because the failure mode is not always visible and partly because the fix is often something small. This article covers the most common priming problems we encounter with PDMS and glass chips, and the steps that resolve them in most cases.
Air bubble entrapment ¶
Air bubbles trapped in the channel during priming are the most common cause of flow failure. They form when the chip is loaded too quickly, when the inlet tubing is not fully purged before connection, or when the chip has been stored in a low-humidity environment that has allowed the PDMS to partially degas. The fix is to prime slowly, at a flow rate well below the intended operating rate, and to use degassed buffer. If bubbles persist, a brief vacuum treatment of the chip before priming can help.
Channel wetting and surface hydrophobicity ¶
PDMS is inherently hydrophobic, which causes aqueous solutions to bead at the channel entrance rather than flow through. Oxygen plasma treatment makes the surface temporarily hydrophilic, but this effect diminishes within 30 to 60 minutes of treatment. If your chip was plasma-treated more than an hour before priming, the surface may have reverted. A short re-treatment, or priming with a low-concentration surfactant solution followed by a buffer wash, usually resolves this.
Flow rate calibration for droplet generation ¶
Droplet size in a flow-focusing geometry is determined by the ratio of the dispersed phase flow rate to the continuous phase flow rate. If the droplets are larger or smaller than expected, the first thing to check is whether the syringe pump is delivering the programmed flow rate accurately. Pump calibration drifts over time, particularly with small-diameter syringes. Gravimetric calibration, weighing the output over a fixed time, is more reliable than trusting the pump display.
Chip-to-chip variability ¶
Even chips from the same fabrication batch can show variability in channel dimensions of plus or minus five microns, which affects droplet size and flow resistance. If you are running a series of experiments that require consistent droplet size, it is worth characterising each chip individually before use. We inspect every chip we dispatch under a stereo microscope, but dimensional variation within tolerance is normal and should be accounted for in your experimental design.
When to abandon a chip and start fresh ¶
If a chip has been primed, used, and then stored for more than 48 hours, the risk of contamination and channel fouling is high enough that starting with a fresh chip is usually more efficient than attempting to clean and re-use it. PDMS absorbs small molecules from solutions that have passed through it, which can affect subsequent experiments. For single-use applications, treat each chip as single-use.
If you are working with a new chip design and encountering priming problems that the steps above do not resolve, we offer microfluidic troubleshooting as part of our chip analysis sessions. Bring the chip and a description of the failure mode and we will work through it with you.