Question

The most commonly used stain for visualising/observing the D fragments is:

• A. Ethidium Bromide
• B. Coomassie Brilliant Blue
• C. Safranin
• D. Crystal Violet

Hint:

EtBr intercalates between D base pairs and fluoresces orange under UV light.
Always handle EtBr with extreme care as it acts as a potent mutagen due to its intercalating mechanism.

Answer 1

The Correct Option is A

Step 1: Understanding the Question:
The question asks to identify the fluorescent chemical dye standardly used in gel electrophoresis to visualize nucleic acid fragments such as D.

Step 2: Key Formula or Approach:
Visualization of nucleic acids relies on intercalating agents that bind between base pairs and fluoresce brightly under ultraviolet (UV) illumition.

Step 3: Detailed Explation:

• Mechanism of Ethidium Bromide (EtBr): Ethidium bromide is a plar fluorescent molecule that intercalates non-covalently between adjacent nitrogenous base pairs of double-stranded D.

• Fluorescence Enhancement: When exposed to UV light (wavelength $\sim 300\ \text{nm}$), EtBr absorbs UV radiation and emits bright orange-red fluorescence ($\sim 590\ \text{nm}$). Intercalation into D increases the fluorescence yield of EtBr nearly 20-fold compared to free dye in solution.

• Evaluation of Other Options:

• Coomassie Brilliant Blue: A dye commonly used for staining proteins in polyacrylamide gels (SDS-PAGE).

• Safranin: A counterstain used in histology and Gram staining of bacteria.

• Crystal Violet: Primary stain used in Gram staining to classify bacteria based on cell wall composition.

Step 4: Fil Answer:
Ethidium bromide (EtBr) is the standard intercalating fluorescent dye used for detecting D fragments in agarose gels.