Laboratory experiment - extraction of DNA from strawberries

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Introduction

DNA, short for deoxyribonucleic acid, is present in all living organisms’ cells. It contains a set of instructions that direct the activities of the organism’s development and function. (Buddies, 2013) It is located within a nucleus; a membrane-bound organelle. (University of Queensland, 2011) Surrounding the nucleus, there is the cell wall, mitochondria, vacuoles, endoplasmic reticulum, Golgi apparatus, lysosomes and etc. DNA is composed of three parts: nitrogenous bases (adenine, thymine, guanine and cytosine), sugars and phosphates which form a double helix with the linkage of hydrogen bonds. (University of Queensland, 2011)

In this lab experiment, fresh strawberries were used because strawberry cells could yield more DNA than any other fruit for the reason that they are octoploids. (Buddies, 2013) This means that each strawberry cell has eight copies its genome; hence they are able to provide a greater amount of extracted DNA for students to see. (Buddies, 2013) Strawberries also contain tiny enzymes, pectinases and cellulases, which are able to help to break down cell walls and make the DNA extraction process easier and more efficient. (Sweeney, 2012) This activity will demonstrate how DNA can be separated from all the other parts of the cell using common household materials. The purpose of this experiment is to learn how to extract strawberry DNA by only using everyday household products and for students to see a large sample of visible DNA because it is predicted that strawberry DNA will be successfully extracted and will become visible to the naked eye.

Materials and Methods:

Three strawberries were put into the microwave and heated for about 12 seconds. Next, green stems were removed, and the strawberries were crushed and mashed into strawberry juice by a blender instead of using hands for a better result. Then, the strawberry juice was poured into a Ziploc bag along with 2 squirts of buffer (a mixture of Dawn dish soap, salt and tap water.) Followed after, the solution was mixed within the Ziploc bag and it was poured into a clean beaker through a big chunk of cheese cloth that was folded twice for best filtration results. Afterwards, chilled 99% ethanol was slowly and carefully poured into the smaller beaker, not disturbing the strawberry mixture (ethanol droplets rolled down the sides of the beaker slowly.) Observations took place after ethanol was poured, and the precipitate was collected with toothpicks. Results and observations were recorded.

Results:

Materials used

BEFORE

AFTER

Strawberries

Red, with seeds and green stems

Smells fruity, and looked fresh

Heated by microwave for about 15seconds

Crushed by a blender,

Liquid, red, strawberry slush

Seeds and strawberry meat mixed together

Buffer

Clear liquid; transparent solution

Nose-piercing smell; smells a bit salty

Mixed in with the strawberry solution

Looks like red slush; fully mixed

Ethanol

Clear and transparent liquid. Icy cold. Nose-piercing smell. 99% alcohol

Alcohol creates another phase with the strawberry solution. One layer of clear liquid on top of strawberry juice.

A visible line of division between the two phases. Air bubbles were present

Precipitate

Clear, pinkish string like DNA clumps.

Looks like noodles.

Have a smooth touch to it, and could be easily picked up with a toothpick.

After adding the chilled ethanol to the filtered strawberry mixture, two phases became visible; ethanol phase and strawberry solution phase. There was a visible dividing line between them. Within the middle section of the two phases, precipitate formed. Strings of clear and white gooey substance rapidly rose to the surface of the ethanol while the rest of the mixture remained the same.

Discussion:

The precipitate formed in the experiment was strawberry DNA. When they were extracted from the strawberry cells, they appeared to be sticky, algae-like, clear and pinkish substances. Webs of DNA could be seen; floating on the surface of the ethanol, and they proved this experiment to be successful. The following are the reasons why this was a successful experiment.

First of all, strawberries were mashed and crushed in the very beginning because it will help to physically separate the individual strawberry cells. (Buddies, 2013) This process is also able to help to break down cell walls, cell membranes and nuclear membrane; allowing the DNA that lies in the nucleus to escape into the solution. By blending the strawberries into tiny pieces and making strawberry juice, cell organelles like mitochondria, vacuoles and lysosomes will also be separated and mixed into the solution. (Sweeney, 2012) Next, droplets of a buffer that consisted dish detergent, warm tap water and salt were added to the strawberry solution.

Dishwashing liquid played an important role this lab activity because it causes strawberry cells to burst open, or lyse, therefore making the DNA in the nucleus to release into the strawberry juice. (Sweeney, 2012) Just like how dish detergents could dissolve fats and lipids to clean plates and bowls, the chemicals in the detergents also have the ability to dissolve the phospholipid sections of the cell walls and proteins from nuclear membranes during DNA extraction. (Buddies, 2013) This process of cell walls breaking apart is called cell lysis, and with the protective barriers being disrupted, DNA and other contents of the cell will be allowed to flow into the solution. (Sweeney, 2012) This leads to the third step in DNA extraction.

The reason why salt, or NaCl, was necessary in this experiment is that it can create an environment where DNA strands could gather up and clump together; which would result in more visible DNA strands at the end. (Wasserman, 2010) The salt also causes some quantities of the cellular debris from cell lysis to precipitate out of the strawberry mixture while still keeping DNA undisturbed in the solution. (Wasserman, 2010) Another reason why salt was used is that sodium chloride helps to break protein chains that are bound around nucleic acids and prevents them from precipitating along with the DNA when ethanol is added. (Buddies, 2013) The last and most important reason of all is that the phosphate compounds (PO43-) in DNA molecules are negatively charged, and they could be neutralized by the positive NaCl ions. (Wasserman, 2010) This is an extremely important role because without this neutralization, the phosphate ions would remain negatively charged in the aqueous solution and ethanol would not be able to pull and precipitate out the DNA clumps. (Buddies, 2013)

Warm tap water was added to the buffer solution because the warmth would speed up the chemical reaction of cell lysis and as well as the neutralization of NaCl and phosphate ions. (University of Queensland, 2011) Filtration took place right after. This is because the salt in the buffer solution caused many cell debris and organelles to separate out. (Buddies, 2013) When the mixture is being poured and filtered out through layers of cheese cloth, the bigger cell residues that are not needed would be trapped and separated from the liquid solution. (Buddies,2013) The DNA, along with the strawberry mixture would pass through and flow down the small beaker.

Ethanol was the last factor that made DNA precipitate. DNA and water molecules are both polar molecules and according to the rule “like dissolves likes,” DNA could be easily dissolved in water. (Zumbo, 2012) However, after NaCl cations neutralized the phosphate backbones of DNA, the bond between DNA and water molecules had decreased by a great amount. Compared to water, ethanol has a lower dielectric constant. (University of Queensland, 2011) With the addition of ethanol with a concentration more than 70% into the filtered solution, it would increase the intermolecular forces between the Na+ and phosphate ions. (Buddies, 2013) Instead of neutralization, the ions would join together and form a stable compound- precipitate would be formed during this process. In conclusion, the addition of ethanol would make the DNA strands to rise up to the surface, to precipitate and to be seen with the naked eye. (Zumbo, 2012)

The reason why the ethanol was chilled and iced is because this would increase the yield of DNA extracted. (University of Queensland, 2011) Since DNA strands are held together by hydrogen bonds, without the protection of nuclear membranes and cell membranes, they will become very fragile in warm environments. (Zumbo, 2012) Cold ethanol also helps to slow down the activity of DNases, or restriction enzymes that protect cells from viruses by destroying any DNA in the cytoplasm. (Zumbo, 2012) Therefore, chilled ethanol would protect the DNA strands from damaged and subsequently leading to a greater yield of extracted strawberry DNA. (Buddies, 2013)

Uses for Extracted Strawberry DNA

Not only does strawberry DNA provide students with learning and biology knowledge, it also helps out the society in many ways. For example:

  • Use the DNA of a highly disease-resistant strawberry’s genes for research purposes (Sweeney, 2012)
  • Studies revolving the evolutionary history of strawberries could take place (Sweeney, 2012)
  • Genetic research could also take place by studying the DNA strands of strawberries. (Some chemicals in strawberries are known to slow down the growth of some tumors). (Sweeney, 2012)

Conclusion:

This lab activity was a success, but there are some possible steps to take for a higher yield of extracted strawberry DNA. During the filtration process, students should have filtered out the useless strawberry cell debris more carefully. This way, they would have gotten a clearer DNA solution, which would then result in a faster and more dynamic reaction between ethanol and the filtered solution.

Just like the predictions in the beginning of this lab activity, the result was a large quantity of clear, pinkish and slimy strands of DNA that looked like spaghetti noodles. Despite of the simple procedure, the results were still extremely obvious, even to the naked eye. It was really easy to see the white DNA strands within the reddish-pink strawberry juice solution. Overall, it was a successful and interesting experiment, and a decent amount of knowledge was gained throughout the process.

Bibliography

Buddies. (2013, January 31). Squishy Science: Extract DNA from Smashed Strawberries.Scientific

American. Retrieved March 29, 2014, from http://www.scientificamerican.com/article/squishy-

science-extract-dna-from-smashed-strawberries/

Sweeney, D. (2012, October 20). DNA Isolation from Strawberries.Department of Genome Sciences.

Retrieved March 30, 2014,

fromhttp://www.gs.washington.edu/outreach/dhillon_dnaprocedure.pdf

University of Queensland. (2011) The University of Queensland.Strawberry DNA extraction experiment.

Retrieved March 30, 2014, fromhttp://www.imb.uq.edu.au/strawberry-dna-extraction-

experiment

Wasserman, R. (2010, May 11). Why Is Sodium Used in DNA Extraction?.eHow. Retrieved March 30,

2014, from http://www.ehow.com/about_6504902_sodium-used-dna-extraction_.html

Zumbo. (2012). Ethanol Precipitation .DEPARTMENT OF PHYSIOLOGY & BIOPHYSICS. Retrieved March 30,

2014,fromhttp://physiology.med.cornell.edu/faculty/mason/lab/zumbo/files/ETHANOL_PRECIP

itation.pdf

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