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I stumbled upon this word in a webpage by bio.libretexts.org:

The dam-methylase of E. coli recognizes the tetranucleotide GATC in DNA and transfers a methyl group (from S‑adenosyl methionine) to the amino group at position 6 of the adenine in that sequence. Note that GATC is a pseudopalindrome, so both strands read the same for these four nucletides in DNA.

What does it mean? How is it different from palindromic sequence?

I've searched google,ncbi and google.books but couldn't find anything.

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    $\begingroup$ Please rephrase the title of your query, so that it actually reads and appears like a question. $\endgroup$
    – Ebbinghaus
    Dec 3, 2016 at 14:57
  • $\begingroup$ 'True' palindromes read the same from 5' to 3' as 3' to 5' on the same strand. Pseudopalindromes read the same as their reverse complements. $\endgroup$
    – Galen
    Dec 3, 2016 at 22:48
  • $\begingroup$ @Galen What is reverse complement? $\endgroup$
    – Tyto alba
    Dec 4, 2016 at 11:49
  • $\begingroup$ @SanjuktaGhosh 1. Reverse order of characters (GATC ->CTAG); 2. Find complement strand (CTAG -> GATC). Note for this particular (pseudopalindrome) sequence, the steps invert each other. $\endgroup$
    – Galen
    Dec 4, 2016 at 18:02
  • $\begingroup$ Try this app to get a feel for what is happening in reverse complementation: bugaco.com/calculators/dna_reverse_complement.php $\endgroup$
    – Galen
    Dec 4, 2016 at 18:05

1 Answer 1

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In DNA there are four nucleotides or "bases", each of which can be matched with a complementary base on the partner chain in the double helix. Thus:

Adenine (A) and Thymine (T) are complementary and Cytosine (C) and Guanine (G) are complementary.

So, a nucleotide sequence is said to be a palindrome if it has an even number of base pairs and is equal to the reverse of its complementary sequence.

For example, in a single strand of DNA the sequence of bases CCATTAATGG is palindromic because the sequence of bases in the complementary strand is GGTAATTACC, its reverse.

A pseudopalindrome is a DNA sequence with an odd number of base pairs yielding a symmetrical complement except at the central base-pair. For example, the DNA sequence ACCTGGT is pseudopalindromic, because its complement on the other strand is TGGACCA, which is its reverse except for the central element.

[There may be some confusion in the literature. The example cited in the question, GATC, is a palindrome, having CTAG as its complement, not a pseudopalindrome.]

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    $\begingroup$ Some of the papers I found also portrayed in your direction. Could you provide a link that I can check out? $\endgroup$
    – Tyto alba
    Dec 4, 2016 at 11:55

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