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Agarose Gel Electrophoresis of DNA: Procedure & Principle

Agarose gel electrophoresis of DNA is a cornerstone technique in molecular biology used to separate, visualize, and analyze DNA fragments of varying sizes. Its principle leverages the negative charge of DNA and the sieving property of an agarose gel matrix. This technique has broad applications in research, diagnostics, and forensics.

Agarose Gel Electrophoresis of DNA: Procedure & Principle
Agarose Gel Electrophoresis of DNA: Procedure & Principle

Agarose Gel Electrophoresis of DNA: Procedure, Principle, and Applications

What is Electrophoresis?

Electrophoresis is a laboratory technique used to separate and analyze charged molecules, such as DNA, RNA, and proteins, based on their movement within an electric field.

How Electrophoresis Works?

  1. The Gel Matrix: Molecules are placed in a gel matrix (often agarose or polyacrylamide). This gel serves as a slightly porous medium.
  2. Electric Field: An electric field is applied across the gel, creating a positive and a negative pole.
  3. Charge Matters: Charged molecules migrate through the gel’s pores towards the electrode with the opposite charge. Positively charged molecules move towards the negative electrode (cathode), while negatively charged molecules move towards the positive electrode (anode).
  4. Size and Speed: The speed of a molecule’s migration depends on two key factors:
    • Size: Smaller molecules navigate the matrix more easily and travel farther in a given time compared to larger molecules.
    • Charge: Stronger charge means a greater pull toward the opposite electrode, resulting in faster movement.
  5. Separation: This differential movement causes molecules to separate based on their size and charge, forming distinct bands or patterns within the gel.

Types of Electrophoresis

  • Agarose Gel Electrophoresis: Primarily used for separating DNA and RNA fragments. Different agarose gel concentrations allow for optimizing the separation of different size ranges of nucleic acids.
  • Polyacrylamide Gel Electrophoresis (PAGE): Used for higher-resolution separation of proteins or smaller fragments of DNA/RNA.
  • Capillary Electrophoresis: Molecules move through thin capillaries filled with a buffer. Highly automated and often used for DNA sequencing.

What is Agarose Gel?

Agarose gel is a gelatinous, semi-solid material used in molecular biology laboratories for separating DNA, RNA, or protein molecules based on their size and charge. Its key ingredient is agarose:

  • Agarose: A natural polysaccharide (complex sugar) derived from seaweed. When heated in a liquid buffer and then cooled, it forms a mesh-like matrix with pores.

How Agarose Gels Work in Science?

  1. Preparation: Agarose powder is mixed with a buffer solution and heated until it dissolves into a clear liquid. This molten agarose is then poured into a casting tray where it cools and solidifies, forming a gel.
  2. Pore Size: The concentration of agarose used determines the size of the pores in the gel. Higher agarose concentrations create smaller pores (good for separating small molecules), while lower concentrations result in larger pores (better for separating larger molecules).
  3. Electrophoresis: In techniques like agarose gel electrophoresis, an electric field is applied across the gel. Charged molecules within samples loaded into the gel will then migrate towards the electrode with the opposite charge.
  4. Size-Based Separation Smaller molecules navigate the gel’s pores more easily than larger molecules, traveling farther from their starting point in a given amount of time.

Using Agarose Gel to Separate DNA

In agarose gel electrophoresis of DNA, the negatively charged DNA fragments move towards the positively charged electrode.

This results in them separating into distinct bands along the gel. Smaller DNA fragments travel further, creating a pattern that allows scientists to determine the approximate sizes of the DNA fragments in a sample.

Principle: Agarose Gel Electrophoresis of DNA

  • Negative Charge of DNA: The phosphate backbone of DNA carries a negative charge, making DNA molecules migrate towards the positive electrode when an electric field is applied.
  • Gel as Molecular Sieve: The agarose gel acts as a porous matrix. Smaller DNA fragments navigate the pores more easily and travel farther on the gel than larger fragments, which face more resistance. This creates a separation pattern based on DNA size.

Procedure: Agarose Gel Electrophoresis of DNA

  1. Gel Preparation
    • Agarose Solution: Agarose powder is dissolved in a suitable buffer (e.g., TBE or TAE) and heated until molten. The chosen concentration (often 0.8-2%) affects pore size.
    • Gel Casting: Molten agarose is poured into a casting tray with a comb placed to form sample wells.
    • Solidification: The agarose cools and solidifies, forming a semi-solid gel.
    • Ethidium Bromide (Optional): This DNA-intercalating dye can be included in the molten agarose for later visualization under UV light.
  2. Sample Preparation
    • DNA Extraction: DNA is isolated from cells or other biological material.
    • Mixing with Loading Dye: DNA samples are mixed with a loading dye, providing density for sample settling and color dyes to track electrophoresis.
  3. Electrophoresis
    • Immersion in Buffer: The solidified gel (within its tray) is placed in an electrophoresis chamber filled with buffer, covering the gel.
    • Loading Samples: Using a pipette, DNA samples are carefully loaded into the wells.
    • DNA Ladder: A sample containing DNA fragments of known sizes is included for reference.
    • Applying the Electric Field: Electrodes are attached (negative near the wells, positive at the far end) and power is applied. DNA migrates toward the positive electrode.
  4. Visualization
    • UV Light (if using Ethidium Bromide): DNA bands glow under UV light, revealing the separation pattern.
    • Documentation: Results are typically captured as a photograph using a gel documentation system or camera setup.
  5. Analysis
    • Distance Traveled: Negatively charged DNA moves towards the positive electrode. Smaller fragments move faster and farther than larger ones.
    • Band Comparison: Comparing migration distances to the DNA ladder provides an estimate of the unknown DNA fragment’s size.
    • Intensity & Quantity: Brighter bands suggest a higher quantity of DNA of that size. Software aids in more precise quantification.

Applications: Agarose Gel Electrophoresis of DNA

  • DNA Analysis & Verification
    • Verifying PCR products: Confirms amplification of the expected DNA fragment.
    • Restriction Digests: Checks predicted fragments obtained after cutting DNA with specific enzymes.
    • Cloning Success: Evaluates if plasmid DNA carries the correct size inserts.
  • Medicine & Diagnostics
    • Genetic Mutations: Electrophoresis can reveal mutated gene fragments with altered sizes.
    • Disease Diagnosis: Detects pathogen-specific DNA for identifying infections.
  • Forensics & Paternity
    • DNA Fingerprinting: Unique banding patterns from repetitive DNA regions aid in individual identification.
    • Relationship Identification: Comparing fragment patterns helps to establish familial relationships (paternity tests, etc.).
  • Diverse Research Applications
    • Gene Expression Studies: Analyze the size and amount of mRNA.
    • Evolutionary Studies: Comparing DNA patterns between species.
    • Purity Checks: Ensuring isolated DNA isn’t contaminated with RNA or other material.

Considerations & Optimization: Agarose Gel Electrophoresis of DNA

  • Agarose Concentration: Affects separation range; use higher concentrations to resolve smaller fragments, lower for larger.
  • Voltage: Impacts run speed and resolution. Balance separation needs with the risk of overheating.
  • Buffer Choice: Affects conductivity and separation. TAE is better for large DNA, TBE for small.
  • Safety: Ethidium bromide is a mutagen; consider safer dye alternatives and good lab practices.


Agarose gel electrophoresis is a robust and versatile technique. While the core method is relatively simple, optimization and careful application ensure accurate and meaningful results for a wide variety of investigations in the science of DNA.

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