On-chip Electrophoresis Devices: Chip Maintenance

• Do properly pre-treat your channel surfaces.  First time you use a glass chip, treat the surface with, say, NaOH to establish a repeatable, high surface charge density.  A recommended cleaning and surface treatment is to rinse channels with 100 mM NaOH for 15 minutes, then 15 minutes with filtered deionized water (DI).  After this, you can introduce your buffer of choice, flush with it for another 15 min, wait some time, and then flush again with buffer.  We have seen measured zeta potentials take more than 2 hrs after introduction of a new buffer to equilibrate. 
• Do rinse/clean your chips often. If you are re-using your chips for multiple experiments (as most of us do), be sure to carefully clean and rinse your chip before and after each experiment (e.g., you might occasionally repeat the "break in" procedure above). Use DI, buffer, and/or a strong base solution.  Remember that surface charge and resultant zeta potential can vary depending on the history of your chip.  You can use a vacuum pump to repeatedly flush/refill wells.  As a check, you might run electroosmotic flow with a field of, say, 500 V/cm until the measured current stabilizes (this is very important for very small channels of order 1 um depth or less).  
• Don't quickly give up on a clogged chip.  Try mating the barbed fitting of an empty (air filled) syringe to an Upchurch fitting (see below).  You can use high pressure to try and push the liquid in the reservoir to clear the clog.  
• Don't store glass chips dry.  Instead, store them with channels filled with DI and at the bottom of a small container partially filled with filtered DI.  We have found that this is the best way to keep them clean; it prevents electrolytes from crystallizing in the channels.
• Doom:  Cleaning/wiping a chip with ordinary tissue paper can scratch a glass microchip, this can reduce the quality of your optical access. Wipe your chip with lens paper.