If currency exists in a solenoid, we can know the polarity.
However, there is no currency in DNA.how to define its polarity then?
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1$\begingroup$ DNA is never structured so that both 5' ends are at the same side, the strands are always antipolar to each other. The structure doesn't work in the opposite direction. Think about a 2-way road: you can define a direction ("polarity) for each side of the road. Proteins that interact with DNA in a directional way are just like the cars on the road: they could feasibly go in either direction with respect to the whole molecule. $\endgroup$– Bryan Krause ♦Apr 7, 2017 at 17:49
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1$\begingroup$ @BryanKrause I hate the word always ;) $\endgroup$– canadianerApr 7, 2017 at 19:33
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1$\begingroup$ @canadianer Ugh, you're right, I hate it too and chastise others - you caught me. I even used italics to emphasize my mistake. Ok so...in most forms of DNA, like the common helix people are most familiar with, the ways you are usually going to learn about it in a basic molecular biology class, the strands are antipolar :) $\endgroup$– Bryan Krause ♦Apr 7, 2017 at 19:54
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1$\begingroup$ @BryanKrause Haha, yes the italics were particularly damning. Didn't want to be overly pedantic, but the counter examples are interesting. Of course, you're right in almost every instance. $\endgroup$– canadianerApr 7, 2017 at 20:27
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1$\begingroup$ @canadianer No worries for the pedantry, totally warranted in this case and I thank you for it. $\endgroup$– Bryan Krause ♦Apr 7, 2017 at 20:37
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1 Answer
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When people discuss the 'charge' of DNA being negative they are referring to the charge within the molecule.
The Phosphates (big red red and blue in the space filling diagram) have a negative charge and make the DNA both water soluble and negatively charged.
One can also talk about the 'directionality' of DNA which simply means that all DNA is 'read' and synthesized in the 5' to 3' direction (referring to the sugar backbone carbon). That's simply how all enzymes make DNA and RNA molecules and how we define the direction of the DNA code.
As far as I know there is no current running through the DNA itself and no pole in that sense.
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1$\begingroup$ "When people discuss the 'charge' of DNA being negative they are referring to the dipole moment within the molecule." The way this is worded seems misleading. Does DNA even have a net dipole moment? Or if you meant the individual dipole moments of each nucleotide, perhaps "moment" should be pluralized. It is also misleading because a net charge (such as DNA's negative) is not required for a dipole moment to exist. Furthermore, a molecule may possibly have multiple charges within it, and not have a net dipole moment (if the charges are arranged symmetrically). I think it would be far better $\endgroup$ Apr 8, 2017 at 21:27
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1$\begingroup$ to discuss the negative charge here without trying to associate it with dipole moments, because the two are not correlated here. $\endgroup$ Apr 8, 2017 at 21:28
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$\begingroup$ @electronpusher A DNA molecule is single-stranded, and has a negative net-charge because of the phosphates and I'm not aware of a symmetric positive charge. I agree a net-charge isn't necessary for a dipole moment, but wouldn't a net charge existing mean that a dipole moment must exist? $\endgroup$– ArtemApr 9, 2017 at 22:13
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$\begingroup$ The symmetry would be from a like charge, for instance molecule with a negative on the right side and a negative on the right side could have no net dipole moment (assuming the atomic arrangement is symmetrical as well). Whether a single strand of DNA has a net dipole moment would depend on its configuration. If it adopted a spiral configuration, like it does as half of the helix, then the negative charges on the phosphates would all average out spatially. That is, if you looked straight down the helical acid, you wouldn't see any point on the circular cross section that has more $\endgroup$ Apr 9, 2017 at 23:53
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$\begingroup$ charge than the rest of the points (assuming a sufficiently large number of nucleotides). By the way, here is an example of a net-charged molecule with no net dipole moment: (en.m.wikipedia.org/wiki/Cyclopentadienyl_anion?wprov=sfla1). $\endgroup$ Apr 9, 2017 at 23:55