Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond?

Is it that they are only relatively hydrophobic?

This forum explains it but does not give an example of the structure.

  • 5
    $\begingroup$ They are not hydrophobic.. They are quite water soluble. See this data sheet for adenine. $\endgroup$
    Jul 27 '15 at 4:55
  • 6
    $\begingroup$ @AliceD This is about biological molecules, I see no reason why it would be off-topic here. $\endgroup$ Jul 27 '15 at 10:08
  • 2
    $\begingroup$ @MadScientist But this is about solubility, so these are physical properties of the molecule. This fits better into chemistry or physics. $\endgroup$
    – Chris
    Jul 27 '15 at 10:23
  • 3
    $\begingroup$ @AliceD Nitrogenous base generally refers to the nucleobases in RNA and DNA, and those are certainly biological molecules. The question about hydrophobicity and hydrogen bonding also have biological implications. $\endgroup$ Jul 27 '15 at 14:07
  • 3
    $\begingroup$ The term "nitrogenous bases" was confusing; so I fixed it. This is a question on biochemistry and most biochemists would know the answer. I would not consider this off-topic. Note that questions should be pushed to chemistry SE only if they concern certain advanced concepts that are not generally covered in basic biochemistry. $\endgroup$
    Jul 28 '15 at 5:19

These two concepts are not mutually exclusive. You have constructed a false dichotomy. Both of these facts are true:

  1. The electrons in the pi orbitals of the conjugated double bonds in the planar rings are hydrophobic and can "stack" on each other as shown in this drawing of a DNA helix where the bases are shown as planar rectangles:

A model of a kinked DNA helix

  1. The nitrogen and oxygen molecules (either in the rings, or as substituents on the rings) can participate in hydrogen bonds (H-bonds):

H-bonds in Watson Crick base pairs

There are other examples of hydrophobicity and H-bonds co-existing. For example on the interior of proteins.

  • $\begingroup$ I am sorry, I don't understand the answer. Why are both the facts true? I think that is what I want to understand more. $\endgroup$
    – Whitecat
    Aug 6 '15 at 22:43
  • 2
    $\begingroup$ Hydrophobicity and and hydrophilicity aren't yes/no things, they're gradients. $\endgroup$
    – Inhibitor
    Aug 8 '15 at 1:56
  • 1
    $\begingroup$ @Whitecat Most detergents are also hydrophobic and hydrophilic at the same time. $\endgroup$
    – March Ho
    Aug 8 '15 at 7:29
  • 4
    $\begingroup$ I think the confusion here is that no, the DNA bases aren't in themselves completely hydrophobic, but in the region of the planar face of each base is a zone of hydrophobicity. In this way, base stacking becomes favorable where water molecules would otherwise attempt to order themselves to maximize hydrogen bonding with each other. $\endgroup$
    – CKM
    Aug 8 '15 at 13:25
  • $\begingroup$ @Kendall Can you add that to the the answer? $\endgroup$
    – Whitecat
    Aug 10 '15 at 18:08

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