Thursday, 22 August 2019

molecular biology - How to write a palindrome sequence as-wish (create, theoretically) ? (self-answered)


There are specific examples from nature, of palindromic sequences.


But without memorizing them, is there any way to randomly write or create or derive a palindromic sequence for a theoretical discussion?


by the way, Genetic palindromes are not an exact ditto of verbal-palindrome.



Answer



I once developed a method, but it is so-basic and simple that I'm pretty sure it is already discovered. Here I "shared my knowledge, Q&A-style"



Step-1


Write a small sequence randomly.


    5'... A T G C C

Step 2


Write the sequence in opposite-direction, on the next line. It will end at just at the next-place of last place of previous sequence, i.e.


         -------->


5'... A T G C C


C C G T A ...5' .

<-------------

Step-3


Fill-in-the blanks following base-pair rule, and the sequence is now ready.


5'... A T G$\:$ C C$\:$ | G G C A T ...3'


3'... T A C G G | C C G T$\:$ A ...5'


Addendum (courtesy: user@Another'HomoSapien')



The previous method was similar way we usually read a verbal palindrome (though unlike a verbal palindrome, any reflection-symmetry was Not present ). But there is a rotational-symmetry (2-fold), (rotational symmetry means it contains parts which are superposable on rotation).


So we could create a palindromic sequence using rotation also.


enter image description here


Or could rotate pre-filled up sequence (if exactly follow the user's instructions)


enter image description here


The brown dot indicates the axis of rotational-symmetry of the written-sequence, vertical to the plane of paper.


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