- DNA footprinting (A): This method identifies DNA binding sites of proteins, so it matches with (III) DNA binding proteins.
- Yeast two hybrid system (B): This system detects protein-protein interactions, hence it matches with (I) Protein-Protein interaction.
- DNA Fingerprinting (C): This technique uses VNTR (Variable Number Tandem Repeats) to identify individuals, so it matches with (II) VNTR.
- SAGE (D): SAGE is used for transcriptome analysis, so it matches with (IV) Transcriptome analysis.
Step 2: Conclusion.
Thus, the correct matching is:
\[
\text{(A) (III), (B) (I), (C) (II), (D) (IV)}
\]
Final Answer:
\[
\boxed{\text{(A) (III), (B) (I), (C) (II), (D) (IV)}}
\]