What is a palindromic nucleotide sequence?

The correct answer is Option (2) → A sequence that reads the same on both strands when reading in the same orientation

A word palindrome, such as MALAYALAM, reads the same forwards and backwards. A palindrome in DNA is different: it is a stretch of base pairs that reads the same on the two strands when both are read in the same direction (5′ to 3′). For example, 5′-GAATTC-3′ on one strand pairs with 3′-CTTAAG-5′; read 5′ to 3′, the second strand is also GAATTC. Each restriction endonuclease recognises its own palindromic sequence.

Option (1) A sequence that reads the same in both directions on a single strand — Incorrect. Reading the same in both directions on one strand describes a word palindrome, not a palindrome in DNA. The book contrasts the two.

Option (2) A sequence that reads the same on both strands when reading in the same orientation — Correct. The DNA palindrome reads the same on both strands when the orientation of reading is kept the same.

Option (3) A sequence that cuts only one strand of the DNA — Incorrect. A sequence does not cut DNA. Cutting is done by a restriction endonuclease, which cuts both strands at its recognition site.

Option (4) A sequence that forms a loop in the DNA structure — Incorrect. A palindrome is defined by its base sequence on the two strands, not by forming a loop. The book's example is a straight stretch of base pairs.

NCERT Extract:
Restriction Enzymes – “… Do you know what palindromes are? These are groups of letters that form the same words when read both forward and backward, e.g., “MALAYALAM”. As against a word-palindrome where the same word is read in both directions, the palindrome in DNA is a sequence of base pairs that reads same on the two strands when orientation of reading is kept the same.”