**Core Concept**
Acridine orange is a cationic fluorescent dye that selectively binds to nucleic acids, particularly double-stranded DNA and single-stranded RNA, due to its high affinity for the phosphate groups in these molecules.

**Why the Correct Answer is Right**
The mechanism of acridine orange binding involves intercalation between the base pairs of DNA or RNA, resulting in a significant increase in fluorescence intensity. This property makes acridine orange a useful tool for staining and detecting nucleic acids in various biological samples, including cells and tissues. The dye's ability to accumulate in apoptotic cells, where the cell membrane is compromised, allows for the visualization of apoptotic cell populations.

**Why Each Wrong Option is Incorrect**
* **Option A:** Acridine orange does not primarily bind to proteins, although it may interact with them indirectly through its association with nucleic acids.
* **Option B:** Although acridine orange can accumulate in mitochondria due to its lipophilic nature, this is not its primary site of action or binding.
* **Option C:** Acridine orange does not exhibit a high affinity for cytoplasmic structures such as the Golgi apparatus or lysosomes.

**Clinical Pearl / High-Yield Fact**
Acridine orange is often used in combination with other dyes, such as propidium iodide, to differentiate between viable and non-viable cells, highlighting its utility in flow cytometry and fluorescence microscopy.

**Correct Answer: D. Nucleic acids.**