Difficulty: Introductory | Prerequisites: Basic cell biology (cell membrane structure, organelles). Familiarity with DNA as the genetic material helps but is not required.
This exercise sits at the junction of molecular biology and lab technique. You are physically pulling DNA out of fruit tissue, weighing what you get, and then learning how enzymes read and cut that DNA at specific sequences. If you have covered cell structure and know that DNA lives inside the nucleus, you have enough background. The practical skills here (extraction, yield calculation, restriction mapping) come back in genetics, microbiology, and any course that touches biotechnology or forensics.
You mash fruit in a lysis buffer to break open cells and release DNA, then precipitate the DNA with cold alcohol so you can collect and weigh it. Different fruits yield wildly different amounts of DNA per gram of tissue. The yield calculation is simple: milligrams of DNA extracted divided by grams of tissue used.
DNA extraction
The process of isolating DNA from cells by breaking open cell membranes (lysis), separating DNA from proteins and lipids, and collecting it. Think of it as cracking eggs to get just the yolks, except the "yolk" is a stringy white mass of nucleic acid.
Lysis / lysis buffer
Lysis means breaking open cells. The lysis buffer typically contains detergent (to dissolve cell membranes) and salt (to help separate DNA from proteins). In simple terms, it is the soapy solution that pops cells open.
DNA precipitation
Adding cold alcohol (ethanol or isopropanol) to a solution of dissolved DNA causes the DNA to come out of solution as a visible, stringy solid you can spool or pellet. In simple terms, the alcohol makes DNA clump together so you can physically grab it.
Yield (mg/g)
The mass of DNA recovered per gram of starting tissue. Calculated as milligrams of extracted DNA divided by grams of tissue used. This is how you compare extraction efficiency across different tissues on a fair, weight-for-weight basis.
Standard deviation (SD)
A measure of how spread out individual data points are from the group mean. A small SD means the replicates gave similar results; a large SD means they varied widely.
Standard error (SE)
Standard deviation divided by the square root of the number of samples. It estimates how precisely the sample mean represents the true population mean. The more replicates you run, the smaller the SE becomes.
Wet weight of extracted DNA
The mass of the DNA pellet as collected, before any drying step. It includes some trapped water and buffer, so it overestimates the true DNA mass, but it is what this protocol measures.
Weigh the fruit tissue (roughly 20 to 25 g)
Mash tissue in lysis buffer containing detergent and salt
The detergent dissolves the lipid bilayer of cell membranes and nuclear membranes
The salt shields the negative charges on DNA, helping it separate from histone proteins
Filter the homogenate to remove large debris (seeds, skin, pulp)
Add cold ethanol or isopropanol to the filtered lysate
DNA is insoluble in cold alcohol and precipitates as visible white strands
Proteins and most other molecules stay dissolved
Spool or pellet the DNA, transfer it to a weighed tube, and record the mass
Weight of extracted DNA (g) = (tube + DNA) minus (empty tube)
Convert grams to milligrams (multiply by 1000)
Total yield (mg/g) = milligrams of DNA extracted / grams of tissue used
Example from the worksheet: 4.42 g DNA from 24.92 g raspberries = 4420 mg / 24.92 g = ~177.4 mg/g (the worksheet reports 319.7, which uses wet weight in mg directly)
Raspberry gave the highest and most consistent yields (~320 mg/g across both groups, SD = 3.8)
Grape gave by far the lowest yields (0.9 and 4.3 mg/g), likely because grape skin is tough and cells are harder to lyse
Strawberry showed high variability between groups (73.5 vs 295.4 mg/g), giving an SD of 127.0
Banana also showed extreme variability (59.5 vs 322.2 mg/g), suggesting technique or sample differences
Apple was moderately consistent (~70 mg/g, SD = 1.2)
Dragon fruit yielded moderately (22.8 and 59.1 mg/g)
Cell wall composition: some fruits have tougher cell walls that resist lysis
Water content: fruits with high water content dilute the extraction buffer
DNA content per cell: polyploid organisms (like strawberries, which are octoploid) have more DNA per cell than diploid organisms
Pectin and polysaccharide content: these can co-precipitate with DNA or interfere with lysis
Technique variation: how thoroughly the tissue was mashed, temperature of the alcohol, and timing all affect yield
Slight differences in how finely tissue was mashed
Temperature of reagents (warmer alcohol precipitates less DNA)
Ripeness and condition of the fruit sample
Loss of material during transfer steps
These sources of error are why we report standard deviation and standard error alongside the mean
\text{Yield (mg/g)} = \frac{\text{mass of extracted DNA (mg)}}{\text{mass of tissue used (g)}}\text{Standard Deviation} = \sqrt{\frac{\sum (x_i - \bar{x})^2}{n - 1}}\text{Standard Error} = \frac{\text{SD}}{\sqrt{n}}For the yield formula, make sure the DNA mass is in milligrams and the tissue mass is in grams. A common slip is to leave both in grams and get a number below 1, which is technically correct but does not match how the worksheet expects the answer.
DNA extraction is the first step in virtually every molecular biology workflow: forensic analysis of crime-scene samples, paternity testing, genetic disease screening, and GMO detection in food products all begin with pulling DNA out of cells. The same lysis-and-precipitation logic used on fruit in this lab scales up to clinical and industrial settings, though the kits are more refined.
Students often think a higher raw weight of tissue automatically means a higher DNA yield. It does not. Yield is normalised per gram, so what matters is the DNA density of the tissue, not how much you started with.
Students often assume the white stringy precipitate is pure DNA. It is not. Co-precipitated proteins, polysaccharides, and salts are mixed in, which is why this protocol measures "wet weight" rather than pure DNA mass.
Students sometimes think that all cells of the same species contain the same amount of DNA. Ploidy level matters: strawberries are octoploid (8n), meaning each cell contains eight copies of each chromosome, which contributes to higher yields compared with diploid fruits.
Students often confuse standard deviation with standard error. SD describes the spread of your actual data points. SE describes how confident you can be in your calculated mean.
Be ready to calculate yield from raw data (tissue weight, tube weight, tube + DNA weight). The arithmetic is straightforward, but unit conversion trips people up.
Know the purpose of each reagent: detergent lyses membranes, salt neutralises DNA charge, cold alcohol precipitates DNA.
Be able to explain why different tissues produce different yields (cell wall composition, ploidy, water content).
Understand what standard deviation and standard error tell you about your data, and why replicates matter.
If given class data, be able to identify which tissue was most consistent (lowest SD) and which was most variable.
True or false: The detergent in the lysis buffer breaks down DNA into smaller pieces. (False. It breaks down cell membranes. DNA stays intact.)
True or false: Cold alcohol causes DNA to dissolve. (False. Cold alcohol causes DNA to precipitate out of solution.)
Fill in the blank: Yield is calculated as ______ of DNA divided by ______ of tissue. (milligrams; grams)
True or false: A small standard deviation means the replicate values were close to each other. (True.)
Fill in the blank: Strawberries tend to yield more DNA per cell than grapes partly because strawberries are ______ (ploidy level). (Octoploid / 8n)
Q: You extract 3.50 g of DNA from 22.00 g of banana tissue. What is the yield in mg/g?
A: 3500 mg / 22.00 g = 159.1 mg/g
Q: Two groups both used apple tissue. Group A got 69.7 mg/g and Group B got 71.4 mg/g. What does the small difference suggest about the reproducibility of the extraction?
A: The results are highly reproducible for apple. The small difference (SD = 1.2) indicates that technique and sample variation had little effect, and the protocol worked consistently for this tissue.
Q: Why did grape tissue produce such low DNA yields compared with raspberry?
A: Grapes have tough skins and relatively fewer cells per gram of tissue that are accessible to the lysis buffer. Raspberry cells are softer and easier to break open, releasing more DNA. Differences in cell wall composition and ploidy also contribute.
Q: Explain why standard error decreases as the number of replicates increases.
A: Standard error equals standard deviation divided by the square root of n. As n increases, the denominator grows, so SE shrinks. More replicates give a more precise estimate of the true mean.
Q: A classmate claims that using more tissue will always increase the yield (mg/g). Is this correct? Why or why not?
A: This is incorrect. Yield is expressed per gram of tissue, so adding more tissue increases the total DNA mass but the ratio (mg/g) stays roughly the same, assuming technique is consistent. Yield per gram reflects the tissue's intrinsic DNA density, not the amount of starting material.
This material connects directly to restriction enzymes and gel electrophoresis (covered in the second half of this exercise and in later labs). The extraction you perform here is the same first step used before PCR, sequencing, or cloning. Understanding ploidy differences ties back to cell division (mitosis/meiosis) and chromosome biology covered earlier in BIO 120.
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