Q.71 Which one of the following double–stranded sequences will NOT be recognized by
a Type IIP restriction endonuclease?
(A) 5′—GGTACC—3′
3′—CCTAGG—5′
(B) 5′—GGATCC—3′
3′—CCTAGG—5′
(C) 5′—CATATG—3′
3′—GTATAC—5′
(D) 5′—GATTTC—3′
3′—CTAAAG—5′
Option (D) is the correct answer. Type IIP restriction endonucleases recognize palindromic double-stranded DNA sequences, where both strands read the same (5’→3′ direction) within the recognition site. Non-palindromic sequences like GATTTC/CTAAAG cannot be bound symmetrically by these enzymes.
Option Analysis
Type IIP enzymes cleave within or near short (typically 4-8 bp), symmetric palindromic sites.
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(A) GGTACC/CCTAGG: Palindromic (top strand 5′-GGTACC-3′ reads same forward/backward as bottom). Recognized by KpnI (Type IIP).
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(B) GGATCC/CCTAGG: Palindromic (GGATCC matches reverse complement). Recognized by BamHI (Type IIP).
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(C) CATATG/GTATAC: Palindromic (CATATG is self-reverse complement). Recognized by NdeI (Type IIP).
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(D) GATTTC/CTAAAG: Non-palindromic (GATTTC reverse complement is GAAATC, not matching CTAAAG). No Type IIP enzyme recognizes this asymmetric sequence.
Introduction to Type IIP Enzymes
Type IIP restriction endonucleases are essential molecular tools that recognize specific palindromic DNA sequences and cleave within them, producing sticky or blunt ends for cloning. These enzymes bind symmetrically to double-stranded DNA where the 5’→3′ sequence on one strand matches the reverse complement on the other. This palindromic property ensures precise, bidirectional recognition critical for biotech applications like recombinant DNA technology.
Key Recognition Features
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Palindromic sites (4-8 bp) enable dimer formation for cleavage.
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Cleavage occurs within/near the site (unlike Type IIS).
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Examples: BamHI (GGATCC), NdeI (CATATG), KpnI (GGTACC).
MCQ Breakdown: GGTACC, GGATCC, CATATG vs GATTTC
In competitive exams like CSIR NET, questions test palindromic identification:
| Sequence | 5′ Strand | 3′ Strand | Palindromic? | Enzyme Example |
|---|---|---|---|---|
| (A) | GGTACC | CCTAGG | Yes | KpnI |
| (B) | GGATCC | CCTAGG | Yes | BamHI |
| (C) | CATATG | GTATAC | Yes | NdeI |
| (D) | GATTTC | CTAAAG | No | None |
GATTTC/CTAAAG fails as its reverse complement (GAAATC) mismatches, preventing Type IIP binding.
Exam Preparation Tips
Practice verifying palindromes by writing reverse complements. Focus on common Type IIP sites for CSIR NET molecular biology sections. Non-palindromic sequences signal Type IIS enzymes, a common distractor.
