Ebay has everything you need – new RapidCycler PCR machine added to the bench
August 12, 2012 in Posts
Although the goal was to get a conventional thermal cycler for PCR, this unique machine was too interesting to pass up doing a little more detective work on. After reading a bit more about the RapidCycler system designed by Idaho Technology, it seemed to perfectly match what we wanted to do, amplify target sequences of under 1,000 base-pairs. The machine is supposed to be able to do a 30 cycle amplification in about 15 minutes, pretty fast when compared to the hour or more a conventional machine might take.
The difference is, this machine uses a high power halogen lamp and a fan for rapid temperature ramping and cooling. It can drop from a 94C denature temperature down to a 55C annealing temperature in about three seconds. Pretty fast!
It sounds good on paper, and seems to cycle well after a basic test, but it won’t be until we actually run some samples then visualize them on a gel that we can know for sure it works.
If anyone has any experience using a rapid cycler, or experience using glass/plastic capillary tubes to hold samples instead of the traditional plastic PCR tubes, let us know! The one thing I am still a little unsure on is…how exactly to get our PCR mixes and reagents into the little capillary tubes. I asked an Idaho Tech rep and they mentioned there is an “aspirator”, or the equivalent of a mini micro-pipettor, specifically designed to add and remove things to the capillary tubes.
We managed to snag this off ebay, so always be on the lookout for cool machines you can get to add to your lab for a decent price!
Here is a video of it in action right out of the box, we’ll keep you updated as we get some capillary tubes and an aspirator and can actually test it.
Video can go up to 720p, so change the resolution if you want a little clearer image.
Did you still need info on using the rapidcycler? I have been working with them for a decade and can help you with any questions you might have. Just email me.
I do actually! We’re about to test it this week, but I don’t think we’re going to have the capillary tubes we’ll need. I emailed the company and they said they basically discontinued selling them, as this was the first generation machine so to speak. I’m wondering if with modifying the annealing times etc, we could use normal .2mL plastic PCR tubes. I know the heat conduction properties won’t be the same, so perhaps we’ll just need to shell out some money for a peltier based one.
If you look at your 50ml plate–the drop down plastic piece is actually for you to place thin-walled tubes into the chamber and use in PCRs–they will work slower than glass capillaries, but only a little bit.
The 10ul glass tubes worked really well with a 0s set time, but since Idaho Technologies (now BioFire I think) no longer supplies those, everyone I know has moved to 25 ul capillaries, which require about a 1 second stall at the temperature to work really well. Even with that, with top of the line polymerase, we have clocked the rapidcycler at about 250-300 bp per second in extension–so you can finish an 800-100 bp fragment in about 4 seconds of extension, with 1 second stops at denaturation and annealing and 1 second temp ramping–that is about 10 seconds for an entire cycle!
In order to get your mixture into the tubes, since insert the tube tip into the mixture at an angle–the capillary action will draw the mixture into the capillary. Then, seal the ends with a flame source and you are good to go. I use hematocrit capillary bulb pipettes to force the mixture out of the capillary after the PCR step and back into a small 200 ul tube. Cole Parmer can get these for you–they charge me $2.50 per bulb (and you could probably just try out their hematocrit capillary tubes as well–those are (I think) $15 for 200 capillaries or something similar–and they come with the bulb).
E-mail me if you have any additional questions.
We use a number of the IT Rapid Cyclers. We use the Roche 20 uL LightCycler capillaries in the 50uL IT Rapid Cycler port holes with good success. I’ve been working with them for about 8 years now with good success, and our lab has been using the Rapid Cyclers since they came out. Very reproducible and FAST!
-Tom