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Eppendorf themselves and many other companies list on their website two above mentioned sizes of "PCR tubes". As I understand 0.2 ml is by far more widespread and "standard" for PCR, so do they make different machines for 0.5 ml tubes or do 0.5 ml tubes fit 0.2 ml holes? Also, what about incubators and other bio equipment that holds epitubes?

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    $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Mar 15 at 19:49
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    $\begingroup$ I have always done PCR and qPCR reactions in 0.2ml tubes, not aware of any blocks designed for 0.5 ml, but they may exist. But there are other form factors that you have to pay attention to. Some (but not all) qPCR cyclers are made to work with low profile PCR tubes only. Some older machines can only use high profile (standard) tubes, but adapters are available. Some manufacturers have even devised multi-instrument workflows that require both. You also have to pay attention to tube color if you're doing qPCR (when in doubt, stick with clear) and skirting on 96-well plates. $\endgroup$
    – MikeyC
    Mar 16 at 14:09

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The answers are both yes and no.

Many PCR machines come with the block designed to hold both 0.2 and 0.5 ml tubes (e.g. this one from Eppendorf**), or with swappable blocks (e.g. Bio-Rad C1000**), this depends on the manufacturer, the instrument you are looking at using, and what specifications you are looking for. For some machines, such as qPCR ones, there isn't any point in having 0.5 ml tube holes as almost all the assays will be done in 96-well 0.2 ml plates or 384 well plates (0.02 ml; with a different block designed to hold these plates). A large portion of whether you can use different tubes in different PCR machines is down to how the (heated) lid closes - if the block is for 0.5 ml tubes, then the lid will not go down far enough for 0.2 ml tubes, unless it is adjustable. Conversely if it is set up for 0.2 ml tubes, the lid will go down too far for 0.5 ml tubes, deforming them and potentially damaging the machine too.

Static temperature incubators, such as thermomixers (Eppendorf brand**) often only come in one tube size (e.g. Eppendorf ThermoMixer F), but there are thermomixers that come with swappable tube holders (like the ThermoMixer C), with anything between 0.5 ml - 50 ml tube holes and even plate holders.

For tube racks, it depends again - some do, some don't. Many 1.5 ml tube racks can be flipped over to expose 0.5 ml tube holes, but it depends on the brand. You can certainly buy racks for 0.2 ml tubes (usually in 96-well format), but 10 ul - 200 ul tip boxes work well for this purpose too. 0.5 ml tubes will fit into 0.2 ml racks, but will be unstable and you won't be able to pack the tubes as densely as 0.2 ml tubes.

** I have no affiliation with Eppendorf, Bio-Rad, nor any other brand and do not endorse or imply endorsement through this post. I also do not I sell or distribute any products - I'm simply an end-user.

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Here's a top-down photo of the heating block from an Eppendorf 6331 Nexus Gradient MasterCycler (source):

enter image description here

Most modern Eppendorf thermal cyclers have a similar block.

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    $\begingroup$ Are those super little ones for 0.02 ml tubes @bob1 mentions? $\endgroup$ Mar 15 at 22:47
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    $\begingroup$ @beardeadclown no. count the super-small holes and you will notice that they are way less than 384. Plates with smaller volume per tube are higher density since they split the positions into 4 smaller ones when going from coarse to finer $\endgroup$
    – masterX244
    Mar 16 at 7:32
  • $\begingroup$ @masterX244 I'm sorry, I didn't get any of that. What's the significance of number 384? Plates I assume mean tube holders, coarse being .5ml and finer being .2ml, and density means holes per area, but I can't see what positions do those super-small holes split into 4 smaller ones. Also, what are those 6 flat holes for? $\endgroup$ Mar 16 at 12:20
  • $\begingroup$ @beardeadclown 384=4x96. Each "position" gets split into 4 smaller ones when raising plate density (except when going from a Basin plate which is a 1x1). Stepping is 6, 24, 96, 384,1536 on the standard plates which all got the same size. And i guess that the 6 flat holes are due to technical reasons. $\endgroup$
    – masterX244
    Mar 16 at 12:27
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    $\begingroup$ @beardeadclown I imagine the smaller holes are to accommodate expansion and contraction of the block as it is rapidly heated / cooled. I'm not sure what the six larger holes are for, but I don't think they are meant to hold tubes $\endgroup$
    – acvill
    Mar 16 at 14:14

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