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Our molecular biology teacher told us that a double helix of DNA was composed of two DNA molecules linked together by hydrogen bonds. The thing is, until now, I always thought a DNA molecule was composed of two strands, those being polynucleotides, both of them being linked together. I can't find a link which is saying the same as my teacher, even if it seems technically correct to call a double helix a dimer of two DNA molecules.

I was curious to know what was the exact terminology.

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  • $\begingroup$ I have provided an answer to this question, but would stress that there is NO "exact terminology" provided in any of the answers because, as far as I am aware, the terminology in molecular biology is based on usage rather than definition. $\endgroup$ – David Jul 6 '20 at 17:24
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As you pointed out, though this may be basic biology, seeking clarification when receiving conflicting information is a good thing. Don't feel embarrassed for asking. :)

.. our molecular biology teacher told us that a double helix of DNA was composed of two DNA molecules linked together by hydrogen bonds.

Respectfully, your teacher is incorrect. A single, double-stranded DNA molecule is comprised of two helical shaped polynucleotides, and are connected together via hydrogen bonding.


Highlight of each polynucleotide

enter image description here


Highlight of hydrogen bonding

enter image description here

And just for further validation, according to Molecular Biology of the Cell, 4th ed., by Alberts B, Johnson A, Lewis J, et al.:

A DNA molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. Each of these chains is known as a DNA chain, or a DNA strand. Hydrogen bonds between the base portions of the nucleotides hold the two chains together.

So, it would seem that your teacher is referring to each polynucleotide, a.k.a. DNA strand, as a DNA molecule. Instead, she should use the verbiage: a single DNA molecule is composed of two DNA strands, which are helical-shaped polynucleotides.

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  • $\begingroup$ the easy way to remember this to think of RNA which is a single stranded polynucleotide. $\endgroup$ – John Sep 29 '17 at 14:04
  • $\begingroup$ @John Well, there's double-stranded RNA too, so... ;) $\endgroup$ – paracetamol Sep 29 '17 at 14:54
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    $\begingroup$ @paracetamol on the flip side, there is single-stranded DNA too, so... :P $\endgroup$ – another 'Homo sapien' Sep 30 '17 at 7:09
  • $\begingroup$ It is easier to understand if we consider RNA. It has higher structural diversity in nature compared to DNA and can form hairpins/stem-loops, double helices, triplexes, quadruplexes and single strands (and a complex containing all these forms). DNA can also form all these structures, BTW. In such cases we do use the terms inter/intra- molecular interactions/hydrogen bonds to distinguish between the double helices and hairpins/stem-loops. $\endgroup$ – WYSIWYG Jun 6 '19 at 8:56
  • $\begingroup$ "double-stranded DNA molecule is comprised of two helical shaped polynucleotides, and are connected together via hydrogen bonding".. This is wrong. Polynucleotide can be a polyribonucleotide or a polydeoxyribonucleotide and DNA is the latter. This definition also asserts that there are helical and non-helical PN and only the helical ones come together to form a dsDNA. Your description of the biophysics is misleading. ssDNA is also considered and called DNA. Plus, a "strand" is not a proper chemical term. $\endgroup$ – WYSIWYG Jun 6 '19 at 9:07
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Hmm, I think that the teacher is actually correct and that the previous explanation, although very nicely referring to text book diagrams, is a little misleading.

The issue here is the nature of a hydrogen bond within the DNA structure. Within a chemical context, generally a molecule is a collection of atoms primarily bonded together via covalent bonds. Hydrogen bonds, by their very nature are transient - if they weren't then the double stranded DNA wouldn't be able to opened for reading! So, a strand of DNA, from the 5' end to the 3' end is one molecule. The reverse complement strand to this is another molecule of DNA. This is important as if you were carrying out a PCR reaction (for example), you would use single, stranded DNA as primers - so this would be a molecule of DNA. Also, if we were to use hydrogen bonds as a means of defining a molecular species, then water would only be one molecule - all of those H2O molecules interact via hydrogen bonds with each other!

But what about the double helix structure? Well this is a consequence of the chemical structure of each nucleotide (and the chemical properties of those atoms), aided by the hydrogen bonding to tightly pack the atoms together - it's a form taken by the thermodynamics of the inter-molecular interactions between the two molecules of DNA.

So, a strand of DNA is a molecule. Two strands (two molecules) of DNA give us the natural, stable, helical form.

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    $\begingroup$ Biologists can be pretty lax when it comes to chemical definitions. Technically it's not a molecule at all but rather a polyatomic ion. $\endgroup$ – canadianer Sep 29 '17 at 16:07
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    $\begingroup$ I don't see how my answer is misleading, and at no point did you directly identify the portion(s) of my response that you then claim to correct. It would be nice if you could do this. $\endgroup$ – user22020 Sep 29 '17 at 18:00
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    $\begingroup$ The IUPAC definition of molecule is "An electrically neutral entity consisting of more than one atom (n > 1). Rigorously, a molecule, in which n > 1 must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state. " goldbook.iupac.org/html/M/M04002.html So unless the two strands are held together too weakly to confine at least one vibrational state (which is not the case) the two hydrogen-bonded strands are one molecule. $\endgroup$ – DavePhD Sep 29 '17 at 18:04
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    $\begingroup$ "Hydrogen bonds, by their very nature are transient .." -- although generally true, there are many opposing examples, with the first to mind being HF. ". This is important as if you were carrying out a PCR reaction (for example), you would use single, stranded DNA as primers - so this would be a molecule of DNA." -- PCR methods don't match how DNA behaves naturally, specifically in that PCR separates both strands entirely all together, whereas naturally occurring separation involves a replication fork, meaning that a great portion, if not almost all, of the DNA remains double-stranded. $\endgroup$ – user22020 Sep 29 '17 at 18:11
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    $\begingroup$ "So, a strand of DNA is a molecule. Two strands (two molecules) of DNA give us the natural, stable, helical form." -- Notice how you keep saying "molecules of DNA", and not "DNA molecules". The OPs teacher didn't use this verbiage, which is important because the two have quite different implications. Additionally, nobody has claimed that the single strands of DNA couldn't be considered as molecules in and of themselves, except perhaps @canadianer =P. No offense, but with respect to you singling out my answer, I believe your response presents a straw man's argument against it. $\endgroup$ – user22020 Sep 29 '17 at 18:31
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This has come up again recently, so let me summarize my own arguments on what I believe is a purely semantic question.

  • In strict chemical terms, according to the IUPAC definition, neither double-stranded DNA (dsDNA) nor its individual separated strands is a molecule but, as stated in the Wikipedia article, a polyatomic ion.

  • If one extends the term ‘molecule’ to ions and considers only the historical criteria of covalent chemical linkage and indivisibility (as applied to small chemical species) one would conclude that the individual separated strands of DNA were molecules, but dsDNA was not — the complete opposite to the assertion in the accepted answer!

  • In practice, however, many authors refer to dsDNA as a molecule, presumably because they regard it as conceptually different to the two (different) single stands. I accept this as usage, but emphasize that it is not based on any formal re-definition of the term ‘molecule’ for molecular biology that I am aware of.

  • Although some text-book authors avoid using the term ‘molecule’ for the individual strands of dsDNA — presumably for clarity in explanation — this use by others is widespread (e.g. in Lakowicz, DNA Technology).

  • It seems absurd to argue that the single stranded DNA genome of, say, SV40 virus is a molecule, but an individual strand of a circular dsDNA plasmid is not. The situation is compounded in the comparable question for RNA. Consider dsRNA viruses, where one strand is synthesized in large quantities: what is being synthesized if it is not an RNA molecule?

  • But likewise it would seem to be absurd to argue that dsDNA is not a molecule but becomes one after, say, chemical cross-linking.

  • In my opinion this question would only be of practical importance if ambiguity could arise from applying the description ‘molecule’ to both dsDNA and its single strands. I see no such ambiguity, per se, and maintain that this is a purely semantic question.

I therefore conclude that assertions that the term ‘molecule’ be restricted to either dsDNA or, conversely, to its individual single strands are both pointless and unjustified.

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