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What is the name of dsRNA (or DNA) where all component strands are identical (i.e. where the complex consists of multiple copies of the same ssRNA)?

Example: 2 identical ssRNAs forming a dsRNA

C C G C G G C G G
| | | | . | | | | 
G G C G G C G C C

Furthermore, is there a different name for it depending on the degree of complementarity (full Watson-Crick complementarity vs. full complementarity with non-Watson-Crick basepairs vs. lower complementarity due to bulges etc)?

My thoughts

You probably wouldn't say "RNA homo n-mer" (for the example above "homo dimer/2-mer") since I assume that would be referring to a 2-nucleotide long ssRNA?

Can you use the terms dimer, trimer, tetramer, 5-mer, 6-mer etc in multiple ways; (a) referring to the binding of nucleotides to each other to form a polymer/n-mer of nucleotides i.e. polyribonucleic acid, and (b) to whole ssRNA or dsRNA binding to each other to form a "dimer"?

You also probably wouldn't refer to it as a "homo duplex" since that refers to something related to chromosomal crossover.

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    $\begingroup$ Welcome to Biology.SE! A few comment to your questions: 1) dsRNA is very rare, afaik it only occurs almost exclusively in some viral genomes; unless you include self-basepairing in structural elemnts 2) As long as there is complete base pairing something like this would be a palindromic sequence, however that term is also used for short elements within a long DNA strand, and doesn't necessarily imply that actual DNA molecule is double stranded. $\endgroup$ – Nicolai Nov 22 '18 at 12:37
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Such a nucleic acid sequence is described as a palindrome or palindromic.

Wikipedia has an entry for palindromic sequence in which it is defined as:

A palindromic sequence is a nucleic acid sequence on double-stranded DNA or RNA wherein reading 5′ (five-prime) to 3′ (three prime) forward on one strand matches the sequence reading 5′ to 3′ on the complementary strand with which it forms a double helix. This definition of palindrome thus depends on complementary strands being palindromic of each other.

It should be noted that this is a description (rather than a name) that is usually applied to segments of larger nucleic acid molecules or to synthetic constructs. I am not aware of a generic name for short dsRNA (or dsDNA) like the one in the question as they are not, to my knowledge, found in Nature and so there has been no reason to devise a name for them. Thus, there are no names for variants either. If you wish to write an article about such things you would need to invent your own terms, but keep well clear of ‘-mers’ (see use of e.g. tetramer).

The sequence presented in the question does not conform to the Wikipedia definition, above, as it has a central mismatch and is therefore not a perfect double-helix. However, as the use of the term palindrome for nucleic acids is a somewhat cavalier extension of the general use of the English word palindrome (an example of which is “ABLE WAS I ERE I SAW ELBA”), I would regard a further minor modification of the Wikipedia author’s definition as unexceptionable.

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  • $\begingroup$ Note that the biological palindromic sequence does not quite match the general meaning of palindrome. The DNA sequence is complementary to its reverse, whereas the normal palindrome is the same as its reverse. $\endgroup$ – mgkrebbs Nov 22 '18 at 17:43
  • $\begingroup$ @mgkrebbs — Yes. But I did note that, didn't I? I wrote "the use of the term palindrome for nucleic acids is an extension of the general meaning of the English word palindrome" and gave a reference to and example of the general meaning of the word, that can be compared to the example in the question for NAs and the reference I provided for that. However, it is worth emphasizing to those not familiar with Napoleonic English. $\endgroup$ – David Nov 22 '18 at 17:55
  • $\begingroup$ I don't agree that palindromic sequence is an extension of the normal word meaning of palindromic because it (in general) violates the one central meaning of palindrome, that its reverse is the same. Since it completely throws out the core meaning and is in conflict with the normal meaning, it is not an extension but rather an alternative meaning. (Palindromes of course have no known biological significance, unlike palindromic sequences.) $\endgroup$ – mgkrebbs Nov 22 '18 at 18:12
  • $\begingroup$ @mgkrebbs — From a linguistic point of view the "use" of the word has certainly been "extended" — from a single string of characters to two strings having special properties in two-dimensions. Only if the 3' end of the first string is joined to the 5' end of the second string do you have a palindrome.in the original sense. I've tried a modification of my own in this spirit, but do suggest alternatives. $\endgroup$ – David Nov 22 '18 at 18:49
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The specific sequence you have posted is not strictly a palindrome since the reverse complement of the top strand is not the same as the bottom strand. Although there is no central body making these definitions, a better term, in my opinion, would be inverted repeat, of which palindromes are a subset (inverted repeats with no intervening sequence). Of course, the final say would be its predominant usage in the literature (of which I am not overly familiar).

Furthermore, the specific sequence you have shown forms an internal loop, though there is no requirement that internal loops be formed from inverted repeats.

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  • $\begingroup$ Yes. That's another way of looking at it. $\endgroup$ – David Nov 23 '18 at 22:53
  • $\begingroup$ …although the description "inverted repeat with intervening sequence" does not capture the mismatch of identical bases in the intervening sequence, which palindrome actually does. $\endgroup$ – David Nov 24 '18 at 14:41

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