The search for the perfect PCR-strip

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The search for the perfect PCR-strip

Article created: Nov 7, 2007
Article by: Jeremiah Faith

PCR-strips are one of the greatest tools in experimental biology. They bridge the gap between high-throughput plate-based experiments and low-throughput tube-based experiments. A PCR-strip is a series of PCR tubes (usually eight 200 ul tubes) connected together. The distance between each tube is the same as that between the wells of a 96-well plate and a multichannel pipettor.

This compatibility with multichannel pipettors allows the utility of a PCR-strip to extend far beyond running a PCR reaction. Sure the strips are a convenient way to run a PCR reaction, since you don't have to mess with a bunch of tiny, individual tubes. But the tubes also make it easy to prepare solutions that will subsequently be loaded with a multichannel pipettor into a 96-well or 384-well plate.

PCR-strips that I always avoid

Some PCR-strips come with an individual cap connected to each tube. These are supposed to be more convenient if you only need to access one tube at a time. But if I only need to access one tube at a time, why not just use single tubes? I don't want to waste my time opening and closing these individual caps, so I only buy PCR-strips with uncomplicated strip caps (i.e. all 8 caps are attached to a strip just like the 8 tubes).

Sometimes you need 12 tubes

If you use the PCR strips for preparing solutions for a plate, it is often necessary to have 12-tube strips. A few companies sell 12-tube versions, but the ones I've seen are outrageously expensive compared with the standard 8-tube strips. Most PCR-tube racks are the standard 8 rows by 12 columns, so just take one 8-tube strip and break it to make two 4-tube strips (this can easily be done by holding the 4th and 5th tubes and twisting the PCR-strip). Place one of your newly created 4-tube strips next to an 8-tube strip in your PCR-tube rack and you've got yourself a 12-tube strip that can be used to load a plate with a multichannel pipettor.

Tubes that are too tight

The first PCR-strips I used were from Bio-Rad (Part No: TBS-0201). These tubes had an excellent seal. So excellent in fact that if I used them a lot for several days in a row, my thumbs would get sore enough that I had to switch over to sealing the strips with my fingers rather than my thumbs. The benefit of these tubes is that secure seal virtually guarantees you wont lose any sample through evaporation in the PCR machine and no liquid will leak out when you invert the tubes to mix solutions in them.

The biggest drawback to these tubes, besides the sore thumbs, is that the tight seal makes it difficult to open the strip without having a little liquid fly out (either from the jerking motion as you break the seal or from the suction caused by breaking the seal). To prevent this (and to speed up your PCR-strip technique in general), it is best if you remove the strip cap with a rolling motion in the direction perpendicular to the PCR-strip (i.e. don't pull the strip-cap from left-to-right; rather push the strip-cap away from you with a rolling motion).

Tubes that seal too lose

BD-falcon low-profile PCR strip
Click image for larger

To prevent destroying my thumbs, I tried the PCR-strips from BD-falcon (Part No: 352129), because I already liked their centrifuge tubes. I had a horrible experience with these PCR-strips. If you have a Bio-Rad iCycler PCR machine, do not use these BD-falcon low profile PCR-strips in it! The strips are very thin-walled, which is good for PCR. However, the tubes are short (low-profile), which combined with their weakly sealing lids causes the ends of the caps to come loose during a PCR reaction. The second time this happened, I knew it wasn't a coincidence and I decided to never use these BD-falcon PCR-strips again (unfortunately, I didn't throw the tubes away and the same problem happened to my girlfriend a year later; oops!). Admittedly, part of my evaporation problem was caused by my not knowing that low-profile tubes don't work well in the Bio-Rad iCycler with its primitive lid sealing mechanism.

The one clever thing about these tubes is that one side is labeled A and the other side is labeled H, so you don't have to mark the orientation of the tube with a marker. However, these labels make it difficult to do the 4-tube + 8-tube = 12-tube strip trick I mentioned above.

Tubes that are (almost) just right

Molecular BioProducts PCR strip
Click image for larger

The tubes I now use for my everyday PCR and solution preparation needs are the PCR-strips made by Molecular BioProducts (Part No: 3418P; I buy them from Fisher). They provide a nice compromise on lid sealing - they don't hurt your thumbs to seal, and they don't pop open in the PCR machine. However, the seal isn't quite tight enough for heavy vortexing (the lids tend to come of a little on the ends, causing liquid to leak out).