Why the two options? (a basic question, but I always buy flat cap, for evaporation issues, and I don't understand why dome cap exists).
I think the domed caps might provide a better fit in some instruments. If you put the heated lid on its place, it pushes onto the caps, flattening them a bit, and thus providing a good contact between the caps and the heated lid. So it ensures that the whole cap is heated, preventing condensation. In some PCR machines, a flat cap might still have a bit of space between the cap and lid. The newer PCR machines will actually have lids that come down until they hit the caps, so they will always provide a good fit, no matter what brand of PCR tubes or 96-wells plates you are using.
Jesica, basic but important question. Actually it varies from instrument to instrument. Like in the new version of Applied Biosystem Veriti PCR you will find the heating lead is having domb shaped curves to fit the respective caps. however it doesn't matter if we use normal one also. so i think result will not vary a lot with any of them.
I think the domed caps might provide a better fit in some instruments. If you put the heated lid on its place, it pushes onto the caps, flattening them a bit, and thus providing a good contact between the caps and the heated lid. So it ensures that the whole cap is heated, preventing condensation. In some PCR machines, a flat cap might still have a bit of space between the cap and lid. The newer PCR machines will actually have lids that come down until they hit the caps, so they will always provide a good fit, no matter what brand of PCR tubes or 96-wells plates you are using.
personally I prefer flat, and use a latex element to put in the PCR. If you are making an optimization with one kind of tube, just keep it
I'm agree with Elisabeth Bik, that domed caps is suited for the PCR machines with higher heat cap which will lead to evaporation problems on flat cap PCR tubes.
I always use domed caps where the thermocycler has a heated lid. The dome shape of the cap is supposed to be better for small amounts of condensate to re-enter the reaction mixture, whereas a flat-shaped cap will encourage larger amounts to form in the cap and stay there.
Seriously, we're scientists, right? So do the exact same reaction (mix up a batch of something that you know works pretty reliably) and aliquot it into 3 of each type tube (3 flat, 3 domed), then put all 6 tubes in the cycler. Run them all out on the same gel, and let us know the results.... :)
In principle I agree with Robert, however, if you are going to do this experiment, you should really test every well of your thermocycler, since it is a known fact that some older thermocyclers vary in performance from well to well (especially outer wells compared to inner wells). The experiment should also be repeated at least 3 times. However, this goes quite a bit further than the original question!
It is my understanding that in response to the pressure applied by the machine's lid the domed cap would spread-up sideways therefore providing better seal between the cap and tube wall. I realized that after running a bunch of small volume (10-15 ul) PCR reactions in the flat cap tubes. They did not provide a 100% evaporation protection. Since then I started using only the domed cap tubes and have no problems anymore.
thank you very much to all of you for answer my question! and I have to mention some important point, here in Argentina, one PCR reaction cost aproximately 2.50 dol per sample! (I want to know how a PCR reaction cost in other countries) so, altough I would plessure to answer this question experimentally, I have to ask to people who has experience on it! :P just to save some money!
I'd forgotten about the "not all wells are equal" problem the older cyclers had. Wow....makes me want to search eBay for an old PE480....
As for evaporation - I always run with a spot of oil on top of the reaction. Harder to do with super small volumes (10-15 ul).....
Thanks for the answers, it helps me also a lot. I agree with the comments of Robert Rumpf and Martin D'Agostino, so I think is important to check if there is differences before run a lot samples, just in case to be sure!!!
According to the description of 'Thermowell' PCR tubes from Corning company, it says:
"Tubes are available with domed caps for efficient heat transfer or flat caps for easy piercing and marking." (see attached handbook, page 2, I highlighted it with yellow.)
I used dome shaped as well as flat cap PCR tubes. However found easy working with flat cap, mainly labelling on top.
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