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Why is there complementary base pairing for DNA? Why can't A pair with C given that they can all form hydrogen bond?

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  • $\begingroup$ When you say that "A pair with C" can you please provide a diagram to show what you mean and how you envision they would fit together? $\endgroup$ – RosieF Sep 29 '16 at 5:10
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It's to do with the physical space the base molecules occupy. There are 2 classes of molecules in DNA bases, purines and pyramidines. One of each always pair together as there will be a total of 3 ring moieties present.

E.g., Adenine (a purine) pairs with Thymine (a pyrimidine).

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If you were to pair 2 pyrimidenes together, you would induce a kink in the DNA backbone and destabilise it.

That said, there is no chemical reason 2 purines or 2 pyrimidines can't hydrogen bond, and they do. This causes mismatches and DNA mismatch repair enzymes recognise the torsion it induces in the DNA backbone and they replace the mismatched base in the proofreading process. If the enzymes miss one mispairing, which can happen as it occurrs often (but the enzymes are very effective), then you end up with a mutation.

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  • $\begingroup$ When you say that two purines can hydrogen bond to form an anti parallel double helix, or alternatively two pyrimidines can hydrogen bond to form an anti parallel double helix, can you draw or describe how you envision the H-bond donors and a H-bond acceptors would align with each other? $\endgroup$ – RosieF Sep 29 '16 at 5:37
  • $\begingroup$ I don't have/can't find a good diagram of this from a quick look. Maybe someone else will find one. It is structurally less stable, so the bonds are likely semi-transient, switching between single, double, and triple bonds depending on molecular vibrations and so on. They all contain O, N and H groups with varying electronegativity though so the most proximal of those are likely to interact. I'm afraid I don't have a very good answer for you though. $\endgroup$ – Joe Healey Sep 29 '16 at 14:15

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