Sciencemadness Discussion Board - Strawberry DNA Extraction - Fun at Home

Strawberry DNA Extraction - Fun at Home

ScienceBum - 12-5-2020 at 15:53

preface: While this certainly has a lot to do with complex biological processes, we are effectively performing a solubility and precipitation exercise. This is one of my favorite home labs to do because it can be done at all ages (with supervision in some cases) and produces nothing very harmful. While I don't go too much into the chemistry, I will go over the general processes. As usual, if I missed anything or was erroneous please let me know.

WARNING/DANGER

If you are allergic to strawberries (as some people are), please ask another individual to assist you with this lab.

Extracting DNA from Strawberries

Step 1: The Ingredients

Although we do need quite a few things for this home lab, everyone should have these lying around the kitchen with the exception of the strawberries. Water, Dish Detergent, Salt, Strawberries (2 are fine but you can scale up or down), 99% Isopropyl Alcohol, a coffee filter or cheese cloth, a plastic sandwich bag, something to stir with, some kind of funnel, and either a large beaker or some non-porous solid container (plastic bucket works fine).

Step 1.5: The Pre-Prep work and Pre-Prep Slides

Prior to the actual lab, I wanted to try making some microscope slides of our strawberry samples before and after. I'm not an expert in microscopy, and although my microscope can go up to 100x magnification, I'm really only able to get halfway decent pictures from 4x and 10x magnification.

When microscope slides are prepared, it's usually beneficial to have them be as thin and as flat as possible. All I had to work with was a kitchen knife so that didn't happen, but I gave it a shot anyway.

Here are the best photos I was able to take from these samples, first at 4x:

Next at 10x:

https://i.ibb.co/3WR8krr/10x-straw.jpg

Step 2: The Actual Procedure

Chuck that rubbing alcohol in the freezer, we want it as cold as possible. Please make sure there are no leaks and we aren't cross-contaminating our food. You can put the bottle in some kind of container to prevent that.

After removing the stems from the strawberries, go ahead and smoosh them in the bag so we can get to the ooey-gooey squishy squish parts of those cells. It should look something like this:

Then we can make our extraction solution, cackling the entire while like a mad scientist. Pour 1/2 cup of water (that's about .12 liters if you hate me), 2-3 drops of dish detergent, and a pinch of salt all to the water. Gently mix it around avoiding making soap bubbles.

Once the extraction solution is made, combine it with the strawberries in the plastic bag using just enough to completely submerse the pulped mass. Gently mix and squish everything together for another few minutes and let them sit to really soak up.

Fun fact: Up until this point, if you enjoy the smell of strawberries like I do you certainly won't enjoy how they smell now

These are decomposition products of aromatics and all those lovely cell organelles being released and breaking down.

Next, we can move onto filtering. Pour the pulped mass into the filter, and let the liquid filtrate pour through. You can use the extraction solution to wash the inside of the plastic bag and get any chunks you might have missed.

Once the liquid slows to a few drops, gently squeeze the filter paper or cloth to get out as much liquid as possible being careful not to break the paper. This can be safely discarded afterwards.

Step 3: The Extraction

At this point, we're ready to extract the DNA. Retrieve the isopropyl alcohol from the freezer (it should be ice cold), and gentle pour in an equal volume of the alcohol into the filtrate solution. It WILL be slow at first as you'll see what start to look like little white crystalline droplets form, but eventually you'll get a large white mass.

The DNA sample (being a double helix) has a lovely tendency to clump up together like a set of headphone wires does. This makes it fairly easy to remove from the top layer either with a stir rod or even a popsicle stick. I went ahead and placed my sample in a test tube for storage.

Step 3.5: The Cleanup

Cleanup is easy. All solid disposable material can be safely thrown in the trash, and all containers used can be washed out with copious amounts of soap and water. For the liquid filtrate, although it does contain a large amount of rubbing alcohol it may be poured safely down the drain followed by 5-10 minutes of flushing with warm water.

Step 3.6: The DNA Slides

My lovely slide making attempt is like a work of art:

Again, I am not the greatest when it comes to making slides, but I did my best and here we have images at 4x and 10x:

Step 4: So What Happened?

Without going into too much detail, DNA stored in cells is pretty tightly packed in there and fairly securely at that. This makes sense as living organisms don't want their genetic codes to be damaged too easily. For things like plant cells which have a cell wall, we need to physically bust open the cells to get into their sweet juicy interiors. We can do this through normal force, although fancier labs might use centrifuges or specialized tools to do the job more efficiently. The end result is identical regardless of how it's done.

Next, we need something to extract the DNA with since we've got a pretty messy and complex organic mess on our hands. Our extraction solution actually does two different things at the same time to make our jobs much easier. First the dish soap will chemically react with the cell and nucleus membranes, finishing our manual process from before and allowing us direct access to the chromosomes and DNA.

Second, the salt will actually react with and help break apart those pesky complex proteins that are also keeping the DNA strands held tightly together. With our soap and salt solution, we are effectively making the DNA free-floating out of the cell. Because we have breakdowns of other organics, this process does not smell very nice

In a fancier lab, they might use different extraction reagents, but again the process and end results are the same.

Once the DNA is free-floating and no longer bound to anything except itself, we can decrease it's solubility by adding something to precipitate it out. Cold rubbing alcohol works fantastically for this. Most of the other crap will not be attracted to the alcohol layer unless it's left to sit.

Step 5: In Conclusion

In theory and practice this lab can be done with virtually any type of cell samples and it can be done safely at home. In most schools, they will use either strawberries or bananas to demonstrate DNA extraction though. The reason for this is because strawberries are octoploids, meaning they have 8 sets of chromosomes, while bananas only have 3.

This means that it's generally very easy to extract large amounts of visible DNA with small sample sizes that can be easily purchased from the store.

Humans have 23 pairs of chromosomes, so DNA extractions only require very small sample sizes.

There were a lot of complexities and processes I avoided since this post is fairly long already, and DNA is a ridiculously complex chain of organic molecule pairs that is deserving of it's own field of study. However, I hope that there were at least a few educational or entertaining things in this post for anyone who has never done this lab before. Thanks for reading

Syn the Sizer - 13-5-2020 at 10:50

Very interesting, is the DNA useful for anything or just a very neat item to add to a collection. Either way I am going to try this out with a few different items.

Tsjerk - 13-5-2020 at 10:55

Be aware the goo obtained here is probably less than 1%, maybe less than 0.1% DNA. I once posted a more thorough isolation somewhere around here. I believe the topic also started with this strawberry isolation protocol.

http://www.sciencemadness.org/talk/viewthread.php?tid=89713

[Edited on 13-5-2020 by Tsjerk]

Syn the Sizer - 13-5-2020 at 11:42

Cool, I will read through the thread and probably try it out.

ScienceBum - 13-5-2020 at 12:31

Quote: Originally posted by Tsjerk

Be aware the goo obtained here is probably less than 1%, maybe less than 0.1% DNA. I once posted a more thorough isolation somewhere around here. I believe the topic also started with this strawberry isolation protocol.

http://www.sciencemadness.org/talk/viewthread.php?tid=89713

[Edited on 13-5-2020 by Tsjerk]

Yeah I figured it wasn't pure

I assume the majority of the mass are proteins we didn't manage to separate off? What's cool is that with some more expensive microscopes you can actually see the base pairs, although I think you need something more powerful than what I have, maybe even an SEM.

Tsjerk - 14-5-2020 at 08:35

No way you can see basepairs with a any microscope. You can see single stands of DNA with a SEM, but only coiled together with a lot of the proteins.

The only way to "see" molecules is with atomic force microscopy.

Abromination - 14-5-2020 at 09:43

Quote: Originally posted by Tsjerk

I never did get too far into that project, the centrifuge had a slight imbalance I couldn’t seem to get rid of. In theory it should work fine, I have used a very similar procedure with professional equipment successfully before.

Tsjerk - 14-5-2020 at 09:57

I mentioned in that thread you don't really need a centrifuge.

Abromination - 14-5-2020 at 10:04

Quote: Originally posted by Tsjerk

I mentioned in that thread you don't really need a centrifuge.

Yep, I had forgotten about that, its been a few years.

ScienceBum - 17-5-2020 at 14:13

In the interests of accuracy, I'd like to make an amendment to several statements made in my original post strictly for those interested in the science:

1) On several occasions I mentioned that the procedures done at home with off the shelf products are effectively the same as those done in the lab. This can be a misleading statement. The processes are almost the same - destroying the sample mass and breaking open the cells to make it easier to chemically separate the DNA.

While lab analysis does require these steps, there are often stark differences - how efficiently the cells are broken apart, the sample size, and even some intermediate workup steps in between I didn't go over. It's a complicated process.

2) The chemical workup and separation.

In my post, the extraction reagent was made by eyeballing ingredients together and mixing dish soap and salt into water. Although it should be obvious, lab analysis does not mix dish soap and table salt into water through the process of guess the liquid volume. They use much more obscure and sometimes dangerous and toxic chemicals for the extraction process, because they tend to be more efficient and selective.

It just so happens that our extraction solution does roughly the same thing as those lab grade chemicals, and they are much easier and safer to handle and work with. Again, although the general process is the same: dissolving the cell and nucleus membranes, reacting the tangled proteins to separate off the DNA, and precipitating out the DNA, there are key differences when done in an industrial setting.

3) The actual DNA.

Yes. We are in fact precipitating out real DNA. However it is not pure in the slightest. As mentioned earlier, the vast majority of that white sticky mess are actually unreacted proteins very tightly wound around the cell's genetic material. From a chemical standpoint, it's an absolute mess and a nightmare to selectively separate off DNA (which is a ridiculously complex chain of compounds itself).

When this lab is done in a home setting, there are three factors to take into consideration: ease of use, toxicity, and end result visibility. This lab is generally done to showcase that through physical and chemical processes we can "see" certain things that otherwise we wouldn't be able to. It is not meant to be a qualitative demonstration on genetics processing, at least when done as a demonstration.

4) Seeing base pairs.

I made an extremely inaccurate and misleading statement. In an effort to showcase what can be seen with a compound microscope, I took some photographs of strawberry and the extracted protein/DNA slides. The DNA slide looks like a white mess of nothing we can focus on, and that's to be expected.

As mentioned earlier, there is no compound microscope that is capable of seeing things on the molecular level. There are different types of microscopes apart from compound ones - we have Scanning Electron Microscopes (SEM) and Atomic Force Microscopes (AFM), both of which are very very expensive and probably beyond the reach of amateur hobbyists on a shoestring budget.

An AFM certainly can see DNA molecules up to a certain point, but not a compound microscope.

5) Beyond the scope of the original post - chromatography

I did not mention a procedure which can be related to this lab because I did not feel it was necessary. An additional step in the purification and analysis of DNA uses chromatography, called DNA-affinity chromatography. I will go ahead and post a link here for those interested in the process:

https://www.ncbi.nlm.nih.gov/pubmed/11725488

As always, if I left out anything important or made a mistake please let me know, and thanks