Which one of the following palindromic sequences in DNA can be easily cut at about the middle by some particular restriction enzyme ?

Question

Accepted Answer

The correct option is 2: 5' GAATTC - 3' 3'-CTTAAG - 5'

This option represents a classical palindromic DNA sequence that is recognized and cleaved by a well-known restriction enzyme, *EcoRI*. A palindromic sequence in DNA is defined as a sequence of base pairs that reads the same backward on the complementary strand as it does forward on the primary strand. For this sequence, reading the top strand 5' to 3' gives GAATTC. Reading the bottom strand 5' to 3' also gives GAATTC (read from right to left). This specific six-base pair palindrome is the recognition site for the restriction endonuclease *EcoRI*, which is one of the most frequently used 'molecular scissors' in biotechnology. *EcoRI* makes a staggered cut between the G and the A on both strands, thus cutting the sequence "at about the middle" and producing single-stranded overhangs known as "sticky ends," which are essential for recombinant DNA technology.

The incorrect option is 1: 5'-CACGTA - 3' 3'-CTCAGT - 5'

This sequence is incorrect for two main reasons. Firstly, it is not a true biological palindrome because the sequence of the two strands does not read the same in the 5' to 3' direction. The top strand reads 5'-CACGTA-3', while the complementary bottom strand reads 5'-ACTGAG-3' (when read in the 5' to 3' direction, opposite to the written 3' to 5' direction), and these sequences are not identical. Secondly, this pair of sequences does not follow the correct complementary base pairing rules for a stable DNA duplex (Adenine always pairs with Thymine, and Cytosine with Guanine). The complement of 5'-CACGTA-3' should be 3'-GTGCAT-5', but the option provides 3'-CTCAGT-5', meaning the structure is not a valid double-stranded DNA molecule.

The incorrect option is 3: 5'-GATATG - 3' 3'-ATGGTA - 5'

This option is incorrect because the two given strands do not form a proper complementary pair as required for double-stranded DNA. The first strand, 5'-GATATG-3', should be paired with its complement 3'-CTATAC-5', following the A-T and G-C pairing rules. However, the option lists the second strand as 3'-ATGGTA-5', which violates the fundamental base-pairing rule of the DNA double helix. Furthermore, even if we were to treat the sequence as a palindrome, it does not read the same 5' to 3' on both strands (5'-GATATG-3' vs. 5'-ATGGTA-3' when read from right to left), and there is no known common restriction enzyme that would readily recognize and cut this non-complementary sequence.

The incorrect option is 4: 5'-CGTTCG - 3' 3'-ATGGTA - 5'

Similar to the other incorrect options, this sequence fails the basic requirement of a complementary DNA duplex. The complement of the top strand, 5'-CGTTCG-3', should be 3'-GCAAGC-5', but the provided bottom strand is 3'-ATGGTA-5'. Since the strands are not correctly base-paired, the sequence cannot exist as a standard, stable double-stranded DNA molecule that a restriction enzyme would recognize and cut. Even if a hypothetical enzyme were to bind, the palindromic definition is not met (5'-CGTTCG-3' on top vs. 5'-ATGGTA-3' on bottom when read 5' to 3' through reversal of the second strand), making it an unsuitable restriction site. Restriction enzymes are highly specific for true, correctly paired palindromic sequences.