Lab Overview: DNA Extraction from a Strawberry and Gel Electrophoresis

Strawberries are octoploid

(8 copies of each chromosome) → more DNA.

Soft tissue

→ easy to break open cells.

Extraction Buffers

1. Detergent

2. Salt

Detergent (like dish soap)

→ breaks down cell membranes and nuclear membranes.

Salt

→ neutralizes DNA’s negative charge, helps it clump

Meat tenderizer or protease

→ breaks down proteins attached to DNA (like histones).

Alcohol (cold ethanol or isopropanol)

→ DNA is insoluble in alcohol, so it precipitates.

Adding extraction buffer effects

1. detergent breaks membranes

2. salt helps DNA clump.

Add protease

 → remove proteins bound to DNA.

DNA Characteristics

sticky and stringy; you can see it in alcohol

Detergent is critical because…

DNA is inside cells

Add cold alcohol

→ DNA precipitates as white, stringy clumps.

Cold alcohol helps..

DNA come out of solution.

 Gel Electrophoresis’ Purpose is to..

• To separate DNA fragments based on size.

• To observe DNA movement in an electric field.

Materials of the Lab

• Agarose gel

• Electrophoresis buffer (like TAE or TBE)

• DNA sample

• Loading dye (to see it move)

• Electric current (positive and negative electrodes)

DNA has a ________ charge

negative

Why does DNA have negative charge?

It’s due to phosphate groups in the backbone

When placed in an electric field…

• DNA moves toward the positive electrode (anode).

• Smaller DNA fragments move faster/farther than larger ones.

Small DNA fragments move…

faster/farther than larger ones

DNA moves towards what end of the electrode?

toward the positive electrode (anode)

• moves to positive side.

What kind dyes migrate in the gel so you can see movement?

• Bromophenol Blue

  • Moves fast, roughly the same rate as small DNA fragments (~300 bp in 1% agarose).

• Xylene Cyanol

  • Moves slower, similar to larger DNA fragments (~4 kb in 1% agarose).

• Orange G (less common)

  • Moves very fast, often with very small DNA fragments.

DNA itself isn’t colored, it’s what?

visualized with stains (like ethidium bromide or GelRed) under UV light.

Electrophoresis allows you to…

compare DNA fragment sizes

Why is alcohol used in DNA extraction?

DNA is insoluble in alcohol, so it precipitates out of the solution

Larger DNA frgaments move..

slower

 What is the role of the agarose gel?

It acts as a sieve to separate DNA fragments based on size.

Why are some DNA stains required to visualize DNA?

DNA itself is colorless; stains bind to DNA and fluoresce under UV light.

If the DNA moved toward the negative electrode, what might be wrong?

The electrodes may be reversed or the DNA charge is neutralized incorrectly.

Why do you need cold alcohol instead of room temperature alcohol?

reduces solubility of DNA and improves precipitation

Why might different DNA fragments from strawberries move at different speeds?

DNA can be cut into different sizes (by enzymes or natural shearing), and smaller pieces move faster through the gel.

 What factors could affect the clarity of the DNA visible in alcohol?

Amount of strawberry DNA, how well cells were broken, alcohol temperature, or presence of proteins/debris

Quick Tips to Remember for the Quiz (READ THEM)

• DNA = negatively charged → moves to positive.

• Detergent breaks membranes.

• Salt helps DNA clump.

• Alcohol precipitates DNA.

• Gel separates DNA by size.

• Smaller fragments move faster.

• DNA is invisible without stain; dyes track movement.

Why is DNA extraction is important to know?

It lets scientists study DNA to understand genetics, test for diseases, solve crimes, improve crops, and do biotechnology research

What is the first step in extracting DNA from a strawberry?

Breaking open the cells (cell lysis) to release DNA

What cell structures are broken down during DNA extraction?

Cell membrane, nuclear membrane, and proteins bound to DNA

Why do we sometimes use soap or detergent in DNA extraction?

To dissolve the lipid membranes of the cells.

Why are strawberries used for DNA extraction in this lab?

They are easy to mash, have lots of DNA, and work well in classroom experiments

What is the role of the electrophoresis buffer?

Conducts electricity and keeps the pH stable.

What can affect the speed of DNA migration in a gel?

• DNA size

• Gel concentration

• Voltage

• Buffer quality

What is a “band” in gel electrophoresis?

A visible group of DNA fragments of the same size.

Why might some DNA not move far in the gel?

If it’s large, tangled, or the gel concentration is high

Cell Lysis

The process of breaking open cells to release DNA.

DNA Ladder / Marker

A set of known DNA fragment sizes used for comparison.

Negative Electrode / Cathode

The side where DNA starts in the gel.

Positive Electrode / Anode

The side of the gel that attracts DNA because it’s negatively charged.