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5'... ATGCC|CCGTA ...3'

3'... TACGG|GGCAT ...5'

or say

5'... AAGT|TGAA ...3'

3'... TTCA|ACTT ...5'

or in generalised way; on each strand;

ABCDEF|FEDCBA

Is there any terminology for such-sort of repeat? A sort of palindromic sequence? A sort of inverted repeat? or mirror-repeat? Does they really exist in nature? (I could not yet found any helpful answer in web, including wikipedia.)

UPDATE

I asked this question because the term "palindromic sequence" is not like the situation in OP but "palindromic sequence" is like this:

5'... ATGCTTTC|GAAAGCAT ...3'

3'... TACGAAAG|CTTTCGTA ...5'

or in general;

5'... A B C D E F | M N P Q R S ...3'

3'... S R Q P N M | F E D C B A ...5'

Where on single-strand there is no symmetry when read (3'---> 5') and (5' ---> 3').

BUT I'm not telling like that. i'm telling about a situation where a reflection-symmetry present in each single strand when read (3'---> 5') or (5' ---> 3').

like

5'... A B C D E F | F E D C B A ...3'

3'... S R Q P N M | M N P Q R S ...5'

From no angle it is a palindromic-sequence because the symmetry is not between 2 opposite strand.

This question came to my mind when for first- time I'd taught about palindromic sequence. I was unable to "literally" match it with verbal palindromes like "AND MADAM DNA" . Rather it was looking to me like

I EAT CAKE

EKAC TAE I

So I thought, if really there exist any sequence literally like "AND MADAM DNA"... whatever if there is any terminology for it or not.


One other Q/A site mentions about a term "mirror repeat", with exact same situation as OP, but gave no reference and further biological importance.

enter image description here http://www.answers.com/Q/Mirror_repeats_in_DNA

Latest revision of Wikipedia also mentions a term mirror repeat and everted repeat, but no further explanation and hyperlink is given.

Another result from google search.

https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg URL: https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg

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It's simply called a palindromic sequence. As you can see here, these sequences are called inverted repeats when random nucleotides are found between the initial sequence and its reverse complement (e.g. TTACGnnnnnnCGTAA), while when there are no nucleotides between them they're called palindromes.

UPDATE
Sorry for my previous answer, I must've missed the point.
I think the situation you showed should be called mirror-everted repeats: to my knowledge, it's a very rare occurring, and I only found some reference in this and this articles, even though no graphic explanation is provided.
P.S. Should you not be able to access the full text of the second article, just let me know.

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  • $\begingroup$ No? I did not find them same. $\endgroup$ – Always Confused Sep 12 '16 at 17:11
  • $\begingroup$ please see my update $\endgroup$ – Always Confused Sep 12 '16 at 17:37
  • $\begingroup$ Sorry about that, just updated my answer. $\endgroup$ – Roberto Preste Sep 12 '16 at 20:10
  • $\begingroup$ Don't worry patterns are always tricky and almost whole of biology is about patterns. $\endgroup$ – Always Confused Sep 13 '16 at 4:16
  • $\begingroup$ @ Roberto The links you gave wasn't helpful because first one (microbiologyresearch.org/error/…) shows page doesn't exist, and second one (sciencedirect.com/science/article/pii/S0923250899001163?np=y) tells to buy (right-now which is not being possible, sad for that) and its preview contains no diagram, so you could provide some diagram etc. from these articles, I'll be grateful $\endgroup$ – Always Confused Sep 13 '16 at 4:21
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As an example of biological symmetry, with my tongue in my cheek, I would call this a mirage.

My reason is that from a structural point of view a sequence of the type you present:

5'... ATGCC|CCGTA ...3'
3'... TACGG|GGCAT ...5'

does not have mirror-image symmetry. This lack of symmetry is because of the asymmetric nature of the phosphodiester bond. The 5' and 3' in your diagram clearly illustrate this fact (3' is not the reflection of 5' either typographically or structurally) If you don’t follow this, draw out each phosphodiester bond in the sequence halves. The base order in the second half may mirror that in the first half, but the directionality of the phosphodiester bonds is the same.

This is not just pedantry but explains why (or is consistent with) such structures appear to have no importance in biology and hence no name. (One only gives names to things one needs to refer to.) One would not expect such structures to occur frequently as they can not be generated by duplication (inverted or not). Those that do occur by chance lack symmetry and would be no more likely to bind proteins than any other sequence (symmetrical DNA structures apparently lending themselves to protein-recognition).

I imagine one could describe such structures in a mathematical sense and give them a name, but if that is your question it should be migrated to a different SE.

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  • $\begingroup$ No not exact in mathematical sense... but rather was finding biological occurrence. I can't confirmedly say there is no biological importance... one i've read about such a sequence in certain biochemistry text... but then I was in hurry situations... I forgot to note-down that . Later-on I could not recall where I've read that. I yet think this question is properly about biology. $\endgroup$ – Always Confused Sep 13 '16 at 10:14
  • $\begingroup$ Thanks yes it is not about mirror-image of stereochemistry. It is just about genetic sequence. $\endgroup$ – Always Confused Sep 13 '16 at 10:16
  • $\begingroup$ If anyone don't know about a thing, how they can start conclude like "it has no importance", or "off-topic" or such. I agree I don't know that is why I am doing a question. But when a professional user doesn't know about a thing yet hurry to decide an action... it really wonders me. (wrote for every moderator, not any specific one) $\endgroup$ – Always Confused Sep 14 '16 at 17:19
  • $\begingroup$ @AlwaysConfused — You asked "Does they really exist in nature?" so a comment on their biological importance was a valid reply. It was not a suggestion that your question was unimportant. I had tried to answer your question from a biological perspective, but felt it possible that you were still interested in the logical aspects. In the latter case I felt it more likely that mathematicians or people interested in language would be more likely to be able to answer your question. Migrating it to another SE group is not rejecting it, just helping you find the appropriate audience. $\endgroup$ – David Sep 14 '16 at 17:55
  • $\begingroup$ Its ok but google search showing me, many source telling about such sequences, and even with same terminology (though none of them directs to proper source). Even another user posted an answer. Then a statement "such structures appear to have no importance in biology and hence no name. " was quite surprising. I wished to keep the question in biology, but if you still think some-other site like maths or chemistry could give better answer, let me know. $\endgroup$ – Always Confused Sep 14 '16 at 18:20

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