Question

Collect five examples of palindromic DNA sequences by consulting your teacher. Better try to create a palindromic sequence by following base pair rules.

Answer 1

Hint: DNA sequencing is the process of determining the nucleic acid sequence, i.e., the order of nucleotides in DNA. It is any method which is used to determine the order of the four bases: adenine (A), guanine (G), cytosine (C) and thymine (T). A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule which when read in a certain direction (e.g. 5' to 3') on one strand matches the sequence in the opposite direction (e.g. 5' to 3') on the complementary strand.

Complete answer:
The meaning of palindrome in the context of genetics is slightly different from the definition used in English grammar. A double helix is formed by two paired antiparallel strands of nucleotides running in opposite directions. These nucleotides always pair in the same way (adenine (A) with thymine (T) in DNA or uracil (U) in RNA; cytosine (C) with guanine (G)). Thus, a (single-stranded) nucleotide sequence is said to be a palindrome if it is equal to its reverse complement. For example, the DNA sequence ACCTAGGT is palindromic because its nucleotide-by-nucleotide complement is TGGATCCA. Reversing the order of the nucleotides in the complement will give the original sequence. Five examples of palindromic sequences are given below.

Enzyme	Source	Recognition sequence
Ecor1	Escherichia coli	5’ GAATTC3’ CTTAAG
BamH1	Bacillus amyloliquefaciens	5’ GGATCC3’ CCTAGG
Taq1	Thermus aquaticus	5’ TCGA3’ AGCT
Alu1 (blunt end)	Arthrobacter luteus	5’ AGCT3’ TCGA
-	-	5’ ACGCGT3’ TGCGCA

Note:
The role of palindromic sequences called ‘clustered regularly interspaced short palindromic repeats’ (CRISPR) found in bacteria and archaea genome basically provides immunity against foreign genetic elements such as plasmids (Barrangou et al., 2007) and phages (Marraffini and Sontheimer, 2008). Certain DNA sequences having twofold inverted symmetry are called self-complementary or palindromic sequences.