In the following palindromic base sequences of DNA, which one can be cut easily by particular restriction enzyme?

5′ CTCAGT 3′ ; 3′ GAGTCA 5′

5′ GTATTC 3′ ; 3′ CATAAG 5′

5′ GATACT 3′ ; 3′ CTATGA 5′

A specific recognition sequence identified by endonucleases to make cuts at specific positions within the DNA is:

Palindromic Nucleotide sequences

The specific palindromic sequence which is recognized by EcoRI is:

5' - GGAACC - 3' 3' - CCTTGG - 5'

5' - CTTAAG - 3' 3' - GAATTC - 5'

5' - GGATCC - 3' 3' - CCTAGG - 5'

Palindromic Sequences

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NCERT Class 12 · Biotechnology Principles and Processes · 3 NEET questions

Most students fail to identify the orientation of DNA strands. If you cannot distinguish 5' to 3' polarity, you will lose marks on Restriction Endonuclease cleavage sites. Precision in reading direction is the difference between a seat in MMC and a repeat year.

The idea

A palindromic sequence in DNA is a base pair sequence that reads the same on the two strands when the orientation is kept 5' to 3'. Restriction enzymes like EcoRI recognize specific palindromic sequences to cut DNA. For EcoRI, the sequence is 5'-GAATTC-3' and 3'-CTTAAG-5'. This symmetry is essential for the enzyme to bind and create staggered cuts.

Why it matters

These sequences serve as specific recognition sites for restriction enzymes to bind and cut the DNA.

NEET lens

NEET expects you to identify the correct 5' to 3' sequence from options. Do not get confused by the complementary strand; always check the 5' to 3' direction of both strands. Memorize the EcoRI sequence as it is the standard example in NCERT. Expect questions on why staggered cuts are preferred for recombinant DNA technology.

Clinical significance

In nature, these sequences are the bacterial immune system. Bacteria use Restriction Endonucleases to degrade invading viral DNA, preventing bacteriophage infection. If this mechanism fails, the bacterial cell is lysed by the viral replication cycle.

Introduction

A palindrome in DNA is a sequence of base pairs that reads the same on the two strands when the orientation of reading is kept the same (5' → 3').

Core concept

Example (NCERT): 5'—GAATTC—3' / 3'—CTTAAG—5'. Reading either strand 5' to 3' gives GAATTC. Each restriction endonuclease recognises a specific palindromic nucleotide sequence in DNA; EcoRI recognises GAATTC and cuts between G and A on both strands, leaving sticky ends. Word palindromes are like MALAYALAM, which read the same forwards and backwards.

Go deeper

Because the cut is made at the same position on both strands, staggered cuts produce complementary single-stranded overhangs (sticky ends).

From Class 10

A palindrome is a word that reads the same backwards, like MALAYALAM. DNA palindromes read the same on both strands.