Question

Which term is commonly used to describe the specific sequence of bases recognized by restriction enzymes?

• A. Clamping sequence or anchoring sequence
• B. Binding sequence
• C. Recognition sequence or restriction site
• D. Target sequence

Hint:

To identify a palindromic restriction site in exam questions:
- Read the 5' \(\rightarrow\) 3' sequence of the top strand.
- Then read the 5' \(\rightarrow\) 3' sequence of the bottom strand (right to left).
- If they are identical, the sequence is palindromic.

Answer 1

The Correct Option is C

Step 1: Understanding the Concept:
Restriction endonucleases (or restriction enzymes) are bacterial enzymes that recognize and cleave double-stranded DNA at specific internal nucleotide sequences.
They act as a defense mechanism protecting bacteria from invading bacteriophage DNA.

Step 3: Detailed Explanation:
Restriction enzymes bind to DNA and slide along the molecule until they encounter a specific nucleotide sequence.
This specific sequence is called the recognition sequence or the restriction site.
Most restriction sites have the following characteristics:
- They are typically 4 to 8 base pairs in length.
- They are palindromic sequences, meaning the sequence reads the same from 5' to 3' on both complementary DNA strands.
For example, the restriction enzyme EcoRI recognizes the palindromic sequence:
\[ \text{5'-G\ A\ A\ T\ T\ C-3'} \] \[ \text{3'-C\ T\ T\ A\ A\ G-5'} \] When the enzyme finds this sequence, it cleaves the phosphodiester backbone of both strands, producing either single-stranded overhangs ("sticky ends") or flat-ended double-stranded cuts ("blunt ends").
Let us evaluate the other options:
- Binding sequence is a generic term for where any protein (such as a transcription factor) binds to DNA.
- Target sequence can refer to the overall region targeted for PCR amplification or gene editing, but is not specific to restriction endonucleases.
Therefore, the specific sequence recognized by restriction enzymes is called the recognition sequence or restriction site.

Step 4: Final Answer:
The correct term is recognition sequence or restriction site, matching Option (C).