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I fail to understand the what exactly is heteroduplex due to unavailability of a suitable diagram. According to wikipidea:

A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms.

Should the following highlighted structure be called heteroduplex?

enter image description here

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  • $\begingroup$ Heteroduplex is also frequently used for duplex formed of strands of different kinds of nucleic acid. For example RNA-DNA heteroduplex. As a matter of fact, that's the only reference of heteroduplex that I am aware of. $\endgroup$ – WYSIWYG Jul 12 '16 at 18:21
  • $\begingroup$ In 'An Introduction to Genetic Analysis. 7th edition' the DNA structures formed from crossing over between homologous chromosomes have been called heteroduplex through out the text. $\endgroup$ – Tyto alba Jul 12 '16 at 18:32
  • $\begingroup$ Perhaps, but as I said, I was not aware of this usage. $\endgroup$ – WYSIWYG Jul 12 '16 at 18:33
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What you've circled is not a heteroduplex. A better name for it would be "crossover" or "junction". Instead, the two duplexes at the bottom of your diagram are what should be labeled heteroduplexes. Your diagram shows one process by which you could generate heteroduplexes starting from homoduplexes.

Here's a better picture from the NCI Dictionary of Genetics Terms that more clearly shows the difference between homo- and heteroduplexes: enter image description here

The two strands in a heteroduplex still have to have a high degree of sequence identity or they won't be able to form into a duplex in the first place. However, because they come from different sources there's likely to be many short subsequences in which one or more base pair is mismatched, causing a deformation as shown.

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  • $\begingroup$ So it is a ds DNA molecule in which the two strands are not fully complementary and derived from two different sources? $\endgroup$ – Tyto alba Jul 12 '16 at 18:02
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    $\begingroup$ Yes, with one edit: it is possible for two strands from different sources to be fully complementary. In general it's just extremely unlikely, although exactly how unlikely depends on your sources and your strand length. $\endgroup$ – tel Jul 12 '16 at 18:07
  • $\begingroup$ What you have shown above should be (and often) called a mismatch instead of a heteroduplex. I have never come across any recent literature that refers to the above kind of arrangement as a heteroduplex. Most modern studies use heteroduplex to mean a duplex formed of different kind of nucleic acids (RNA-DNA, DNA-PNA etc) $\endgroup$ – WYSIWYG Jul 12 '16 at 18:23
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    $\begingroup$ @WYSIWYG It's both! (a mismatch and a heteroduplex, I mean) The fact that there's a mismatch is less important than the fact that the two strands come from different sources (which is something we're assuming for the sake of the diagram). Though I too was unaware of the more expansive definition before I started writing this answer, NCI seems to back Wikipedia up on this. $\endgroup$ – tel Jul 12 '16 at 18:37
  • $\begingroup$ I also was not aware of the definition given in this answer but for the sake of congruence it absolutely makes sense or even has to be that way as two strands of different origin are pairing. $\endgroup$ – AlexDeLarge Jul 12 '16 at 19:22

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