A Cocktail of Biology

DNA is not just found at crime scenes. It’s in every living thing – you, your cat, the bacteria on your hands and the grass under your feet. It’s in every meal you’ve ever eaten and, under the right circumstances, it’s even in your cocktail.

Strawberry picture

Supermarket strawberry. Hell yes I took this hazy photo with a $30 phone and a droplet of water.

The DNAquiri is a cocktail recipe that won Best in Show at the 2011 Science Hack Day San Francisco because it is also a protocol for extracting DNA from strawberries. The recipe calls for only three ingredients – frozen strawberries, pineapple juice and high-proof rum – but the final product is a complex cocktail of curiosities.

This post is another of my recycled school assignments, in which I was given the slightly daunting task of writing a story in the form of a list. I decided the best kind of list is a recipe, and the best kind of recipe is one that involves both science and cocktails. A deep bow and a tip of the hat to Margot at Hypatian Axis for drawing my attention to the quirky back story of the modern strawberry.

1) Strawberries

Strawberries are a convenient source of DNA because they are delicious and they are octoploid. Octoploid means that each cell in a strawberry contains eight copies of every gene. In contrast, human cells are diploid, with only two copies of each gene, one from mom and one from dad. In the same way, strawberry cells have four copies from mom and four copies from dad, and yes, strawberry plants do have parents. In fact, according to G.M. Darrow in The Strawberry: History, Breeding and Physiology,the mother and father of the cultivated strawberry were the stars of an unlikely transcontinental plant romance.

It all started in 1712, when some unusually plump strawberries caught the eye of a French spy in Chile. The spy was Amédée François Frézier, an engineer in the French Army Intelligence Corps who was spying on Spanish defenses in South America. He noticed that the strawberries cultivated by the locals were much larger than European strawberries and selected several specimens with excellent fruit to take back to France.

Although these plants survived an arduous 6-month voyage to Europe, they did not immediately live up to Frézier’s enthusiastic description. The king’s gardener could not get them to reliably produce oversized fruit “as big as a Walnut, and sometimes as a Hen’s Egg”. By choosing only fruiting plants, Frézier had inadvertently selected only females. At that time, nobody realized that strawberry species often have separate sexes, which is relatively unusual for plants. Male plants carry pollen, while female plants bear fruit, so those female strawberry immigrants were effectively infertile. This is where we meet dad.

Dad was the Virginia strawberry, a wild species still common in the Eastern US that was introduced into Europe in the 1600s. While botanical gardens initially struggled to produce Chilean strawberries, enterprising farmers succeeded by alternating rows with other strawberry varieties. These included some male plants with pollen that could fertilize the Chilean females. The Virginia strawberry gave the best results and the descendents of this pairing became the modern strawberry, which is strongly flavored like its Virginian ancestors, but large like the Chileans. Part of the reason the match worked genetically is that while the European strawberry varieties were mostly diploid (with two copies of each gene per cell), both the Virginia and Chilean strawberries were octoploid2.

This octoploid romance means that every cell of a supermarket strawberry is jam-packed with DNA, making it easier for us to extract enough DNA to see with the naked eye. But first, you need to get the DNA out of the cell.

When strawberries freeze, the water in the cells forms ice crystals that puncture the cell membranes. So if you put frozen strawberries in a Ziploc bag and then squash them, warm them to 50°C then chill them again, some of the DNA will spill out of the leaky cells. Force the pinkish mush through a strainer to get rid of the lumps and you’ll have a strawberry cell extract, otherwise known as juice.

2) Pineapples

The strawberry juice contains DNA, but it also contains all kinds of other stuff from inside the cells, including proteins. Proteins translate the genetic information in DNA into action; DNA sequences carry the instructions for making lots of different kinds of proteins, which in turn do many different jobs. But when all those strawberry proteins are released from the cell into the juice, some of those jobs interfere with the process of DNA extraction.

For example, some of the proteins wrap around the DNA strands, winding them into bundles that don’t extract well. Other proteins chop up the DNA. To counter the effects of all these proteins, you can add “protein-chopping” proteins called proteases. Proteases chop other proteins into bits and although they can be found in all cells, they are found in conveniently large quantities in pineapples. In fact, pineapples have such high concentrations they are used in industrial applications. They are even available in the supermarket, sold as a meat tenderizer that works by digesting the collagen protein that gives meat its structure.

Pineapple - up-close (macro)

Pineapple close-up. By Uri_Breitman (Flickr) [CC BY-NC 2.0]

This is also why pineapple has a bit of a bite to it — that burning sensation when you eat too much pineapple is from proteases damaging proteins on the surface of your tongue.

To digest away the protein in your strawberry mush, simply add some cold, unpasteurized pineapple juice and let the proteases do their work. Now your Ziploc bag contains strawberry DNA and strawberry proteins being chopped up by pineapple proteins. But the DNA is still invisible.

3) Rum

Your next step is to force the DNA to stick together into a clump that you can see. To do this you pour a layer of ice-cold, high-proof rum over the strawberry cell extract. “High proof” just means a high concentration of alcohol (ethanol), in this case 70%, which is about twice as high as normal rum.

In watery liquids, such as strawberry guts and pineapple juice, DNA is coated in a loosely bound layer of water molecules (called a “hydration shell”). This coating prevents the DNA, which is negatively charged, from binding the positively charged ions (like the sodium from table salt2) that are also floating around in solution. But ethanol disrupts the hydration shell and makes the DNA more attractive to positively charged ions. Under these conditions, the DNA will tightly bind positively charged ions that neutralize the overall charge of the DNA. Because the DNA molecules are now neutral, instead of repelling each other, they tend to stick to each other, forming much larger, visible blobs (see note 3 below for my original, quite wrong explanation).

Understandably, ethanol at a high enough concentration to cause DNA to stick together is highly toxic to cells (you could use high-proof rum as effective but expensive disinfectant). But the ethanol in your bottle of rum was originally made by cells — yeast cells.

Yeast are fungi, like mushrooms, but they are microscopic, consisting of only a single cell. They excrete ethanol during the process of extracting energy from fruit sugars. Grapes and other fruit are the natural habitat of yeast, at least during the summer. According to scientists at the University of Florence, yeast’s winter home is in the guts of wasps that feed on grapes. These wasps provide a warm and moist refuge from the elements while fruit is out of season and once the fruit ripens they provide transportation to the site of the annual sugar feast.

Yeast on grapes

Grapes. By Scharks [CC-BY-SA-2.0], via Wikimedia Commons

Preventing other microbes from joining in on the feast is part of the reason why yeast cells excrete ethanol. Yeast get their energy from sugar by converting it to ethanol and carbon dioxide, a process called fermentation. Fermentation generates much less energy than respiration, the method that humans use to metabolize sugar, but fermentation is much faster and has the added benefit of producing a toxic by-product, ethanol. When a wasp inoculates a grape with yeast cells, the yeast rapidly convert their surroundings into an acidic, alcoholic soup that is inhospitable to most other microbes.

Humans have taken advantage of yeast’s curious lifestyle to produce alcoholic drinks, but we have also used it to advance scientific knowledge. For example, studies of yeast fermentation overturned Louis Pasteur’s hypothesis that cells were powered by a mysterious vital force that fundamentally distinguished living from non-living things.

The basic unit of life is the cell, which can grow and divide to make more cells. Pasteur had found that some chemical reactions — like fermentation of sugar to alcohol — could only be catalyzed by live yeast. Vitalists like Pasteur argued that live cells possessed a “vital spark” that allowed them to become more than the sum of the biochemical reactions occurring inside their cell membranes.

As recounted by Christian Reinhardt in Nobel Laureates in Chemistry, 1901-1992, Pasteur’s strain of vitalism was dealt a death blow by Eduard Buchner, a German chemist who was trying to extract proteins from yeast cells without damaging the proteins in the process. He managed this in 1896 by grinding yeast with sand and then filtering out the slurry of broken cells to produce a non-living “yeast juice.” There were no yeast cells remaining in the juice, but it did contain many of the biochemicals, like proteins, that had once been inside the cells. To stop this mix from spoiling before it could be used in other experiments, Eduard, who had once worked in a cannery, tried the method that preserves fruit in jams — ­adding a high concentration of sugar. To his surprise, within 15 minutes of adding sugar to the yeast juice, it started to froth like a fermenting beer.

Rising bubbles from yeast fermentation

Bubbling yeast fermentation. By Jim Champion (Flickr: Rising bubbles) [CC-BY-SA-2.0], via Wikimedia Commons

Buchner was able to show that the proteins in the yeast juice could produce carbon dioxide and ethanol from sugar in a way that was identical to fermentation by live cells. Pasteur was wrong, and no vital force was necessary to explain the metabolic activities of the cell. Cells were really just the sum of their parts.

Buchner’s experiments were a key moment in the dawn of biochemistry, the field that uses non-living extracts of living things (like your strawberry juice) to understand the chemical reactions that allow cells to function. One of the most important discoveries of biochemistry has been that many of these chemical reactions are similar in all organisms, and that all living things share the same genetic code. So, once you see a white film form in a layer between the pink strawberry juice and the amber rum, take a cocktail stick, twirl it around in the film and remove a blob of DNA. This unassuming clump of slime is the hidden genetic material that helped make those delicious strawberries. Be sure to give your drink a good stir before you toast the shared heritage between yeast, pineapples, strawberries and yourself.

DNAquiri blob extraction

Blob of unknown identity. By me.

Sad taster’s note and party poopery: I’ve tried the DNAquiri recipe twice and each time have achieved a very respectable yield of white slime and an almost drinkable cocktail (it’s a bit strong for me). However, I’m going to guess that the slime is not actually DNA, but instead is pectin, a cell wall carbohydrate that gives fruit jams and jellies their gel-like consistency. I base this guess on a suggestion from the UK’s National Centre for Biotechnology Education and the fact that the slime isn’t as stringy as I’m used to for DNA. Please weigh in, all you fruit DNA experts! I want to know!

1More party poopery: Darrow’s story about the origin of the three strawberry flowers on the Fraser coat of arms is probably false. Darrow recounts an old myth that Frézier and the Scottish Fraser clan were descended from one Julius de Berry, who was knighted in 916 by the Emperor of France, King Charles the V. According to the legend, de Berry was knighted in reward for his miraculous ability to provide unseasonably ripe strawberries for a feast. He was given a new coat of arms and a new name, Fraise, which is French for strawberry.

2At this point, anyone who has ever done a DNA precipitation before will be all like “where’s the salt???!”  Typically, it is necessary to add salt to the mixture to provide enough positive ions to neutralize the DNA. The creators of the DNAquiri left the salt out so that the final cocktail was not profoundly disgusting, but I suspect that this favors the precipitation of polysaccharides (like pectin) more than nucleic acids. (note added May 25, 2013).

3 This is not the original version of the explanation I had. Embarrassingly, it originally read:

The interior of a cell is watery and DNA is a ”water-loving” or hydrophilic substance that dissolves readily. But just as oil and water don’t mix, hydrophilic substances don’t mix well with “water-hating” or hydrophobic substances, like ethanol. When immersed in ethanol, DNA molecules stick together into much larger, visible blobs.

Then @EricGumpricht called me out on my decision to call ethanol “water hating,” which was convenient for my word limit, but of course, not remotely true — cocktails wouldn’t be much fun if spirits weren’t miscible with water! I was trying to describe ethanol precipitation without turning this into a chemistry lesson and talking about dielectric constants and whatnot, but I failed miserably (as usual, I blame sleep deprivation and my unwillingness to proofread blog posts). I’ve experimented with an explanation that doesn’t mention polarity because otherwise I ended up with a pretty dull essay. If you have taken high school chemistry and are genuinely interested in how ethanol precipitation works, try these much better explanations:

Bitesize Bio: How ethanol precipitation of DNA and RNA works (requires registration)

Paul Zumbo: Ethanol precipitation (PDF)

(note added May 25, 2013).

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2 thoughts on “A Cocktail of Biology

  1. Pingback: Morsels for the mind – 24/5/2013 | Six Incredible Things Before Breakfast

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