In a previous post I presented a simple protocol for collecting plant tissue for DNA extraction in a 96-well plate format. Later on we’ll get to the details of performing the DNA extraction. Before getting to that, we need to talk about the proper way of grinding plant tissue to get a nice, homogeneous powder. Like the subject of the previous post, this is a seemingly-simple step that often goes underappreciated. I promise that I will get around to a protocol for performing an actual DNA extraction sometime soon.
Tissue grinding is one of those things that can soak up hours of time if it doesn’t go right. If samples don’t grind properly, you’ll have to spend a lot of time trying to shake them again and again; you may even need to remove tissue from some wells if they are overfilled, which takes time and opens you up to more risk of cross-contamination.
Clearly, it’s best to grind the tissue properly in one fell swoop, so you can be on your way to the extraction with no problems. The previous post was all about gathering samples in a highly consistent fashion to enable an easy grinding step. Depending on whether you had a lyophilizer at your disposal for the last step, your tissue should now either be dried, or else frozen.
- 96 well deep-well plates (Axygen Scientific # P-9641-1S)
- Liquid nitrogen (if using frozen tissue)
- Spex SamplePrep Genogrinder 2010
- Styrofoam shipping cooler (if using frozen tissue)
- Tongs (if using frozen tissue)
Step 1: Label Racks
The deep-well plates that I listed above have wells that are wide enough to fit our microtiter tubes in, so we will essentially be using them as heavy-duty tube racks. For the rest of this post, I will refer to them as “racks” instead of plates to avoid confusion. The racks that the tubes come with are too flimsy for tissue grinding – after a round or two in the Genogrinder, they will likely self-destruct. For the DNA extraction, you’ll be using anywhere from one to four plates of samples (i.e. up to 384 samples). So, the steps are:
- Label your deep-well racks something like “Grind-1”, “Grind-2” etc., for however many you need.
NOTE: The Genogrinder requires two racks at once, due to its clamp design. So, if you only have a single plate of samples, you should still label two deep-well racks to be used for grinding (more on that below).
- Transfer the tubes into the racks that will be used for grinding. If you have a single plate of samples, split the tubes into two racks, spacing them evenly across each rack for uniform clamping inside the Genogrinder. This is one step that should convince you that the unambiguous labeling of tube strips that we performed in the previous post was a good idea.
Step 2: Deep Freeze
For lyophilized tissue
If you have lyophilized tissue, you may be tempted to put it into the grinder at room temperature. I’m here to tell you that it won’t work – although the tissue is dry, it is still too flexible to grind properly at room temperature. You’ll just end up with large pieces of leaf that are jammed into the bottom or tops of the tubes. Despite this, I can’t emphasize enough how much easier it is to work with lyophilized tissue, because you can grind easily it after letting it sit in a -80° C freezer for a while. So, if you have lyophilized tissue, this part is easy:
- Place tubes in grinding racks in a -80° C freezer for a few hours or overnight.
For frozen tissue
If you’re using frozen tissue, -80° C probably won’t be cold enough for adequate grinding. Unfortunately this means you’ll need to use liquid nitrogen. So, the steps are:
- Pour an inch or so of liquid nitrogen from a vacuum flask into an adequately-sized styrofoam cooler (the square ones used as inserts for shipping refrigerated/frozen lab supplies work well)
- Use tongs to submerge the grinding racks holding the sample tubes in the liquid nitrogen for a minute or so
Step 3: Grinding
Whether you have used lyophilized or frozen tissue, the next steps are the same:
- Quickly transfer the racks into the Genogrinder (I probably shouldn’t have to mention this, but please use tongs and not your bare or gloved hands to do this if the racks are sitting in liquid nitrogen)
- Secure racks in place with the clamping mechanism and close the Genogrinder’s lid
- Grind the samples! I typically run the machine at 1,000 rpm for 1 minute.
After grinding, the samples should have turned into nice, pale-green flaky powder, like the first five tubes in the picture below:
Epilogue, and Reflection
That’s all there is to it. Like I said at the beginning, grinding plant tissue is not rocket science, but doing it properly can save you hours of frustration. You can now:
- Put the sample tubes back in their original (flimsy) racks
- Place the samples back in a freezer for storage, OR
- Proceed directly to DNA extraction
One thing to note is that we can reuse the grinding racks – just check prior to each grinding to make sure that cracks aren’t forming in them. If they are getting cracked, just discard them and use a new set. In general, things tend to break when they are exposed to liquid nitrogen and then immediately shaken at high speeds – don’t be surprised if you need to replace racks often when using liquid nitrogen, or if you need to replace some cracked tube caps.
One final warning: any rack that goes into the tissue grinder should never go into a centrifuge later. Take it from me: you might end up really, really sorry if you ever do this. There’s nothing that can ruin your day quite like having a rack holding tubes full of chloroform shatter inside a spinning centrifuge.