Biology · Biotechnology: Principles and Processes · NEET
Not exactly. A word palindrome (MALAYALAM) reads the same letter-by-letter when you reverse it on the SAME line. A DNA palindrome is different: you must read the SECOND strand in its own 5' to 3' direction, not just reverse the first strand. In EcoRI's site the top strand reads 5'-GAATTC-3' and the bottom strand also reads 5'-GAATTC-3' when read from its own 5' end. So it is the same sequence on two separate strands, each read 5' to 3'.
Take the complement of GAATTC: the pairing strand is 3'-CTTAAG-5'. Now read that bottom strand from ITS 5' end: 5'-GAATTC-3'. Same as the top strand, so it is a palindrome. For GATACT, the complement is 3'-CTATGA-5', which reads 5'-AGTATC-3' from its own 5' end. That is NOT the same as GATACT, so it is not a palindrome. This is why option GATACT was wrong in the NEET 2022 question.
You read 5' to 3' on BOTH strands separately. Because the two DNA strands are antiparallel (they run in opposite directions), reading each strand from its own 5' end is the correct rule. If a sequence reads the same both times, it is palindromic. Just reversing the letters of one strand is a common mistake and gives the wrong answer.
They belong to the same site written on the two strands: 5'-GAATTC-3' pairs with 3'-CTTAAG-5'. CTTAAG is written 3' to 5' there. If you flip and read the bottom strand from its 5' end you again get 5'-GAATTC-3'. NEET 2020 tested this exact trap: the correct pairing is 5'-GAATTC-3' / 3'-CTTAAG-5', and the option that swapped the strand labels was wrong.
A restriction enzyme (a restriction endonuclease) usually works as two identical protein subunits, one on each strand. Because the recognition sequence is palindromic, each subunit sees the SAME sequence on its strand and cuts at the same position. This is what lets the enzyme cut both strands neatly, often a little away from the centre, producing matching sticky ends. No palindrome means the enzyme cannot recognise and cut precisely.
The specific palindromic sequence which is recognized by EcoRI is:
In the following palindromic base sequence of DNA, which one can be cut easily by a particular restriction enzyme?
Try the real previous-year questions from this chapter — each with the answer and a full solution.
It is a stretch of base pairs that reads the same in the 5' to 3' direction on both strands, for example 5'-GAATTC-3' paired with 3'-CTTAAG-5'. Restriction enzymes recognise and cut such sequences.
The most important example is the EcoRI recognition site: 5'-GAATTC-3' / 3'-CTTAAG-5'. Another is the BamHI site 5'-GGATCC-3' / 3'-CCTAGG-5'. NEET most often tests GAATTC.
Write the complementary strand, then read that bottom strand from its own 5' end. If it gives the same sequence as the top strand, it is a palindrome. If not, it is not palindromic.
No. The genetic code is degenerate, unambiguous and nearly universal, but it is NOT palindromic. Only restriction enzyme recognition sites in DNA are palindromic. NEET has set this as a trap option.
Because the enzyme acts as two identical subunits, one per strand. A palindrome lets each subunit see the same sequence and cut symmetrically, usually a little away from the centre, giving matching sticky ends.
