In the molecular structure of a DNA it is seen that purines (adenine and guanine) bind with pyrimidines (cytosine, uracil and thymine) through hydrogen bonds, and this is always between a purine and a pyrimidine. Can't there ever be hydrogen bonds between 2 purines or between 2 pyrimidines?

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    $\begingroup$ There can, but essentially it doesn’t fit into the double helix so well. That’s arguably better suited for Biology. $\endgroup$ – orthocresol Feb 3 at 19:01
  • $\begingroup$ en.wikipedia.org/wiki/Hoogsteen_base_pair $\endgroup$ – Mithoron Feb 3 at 20:34
  • $\begingroup$ The reason that you predominantly find A:T and G:C base pairs in double-stranded DNA is because the DNA polymerase make a reverse-complementary strand when they copy one strand of DNA. You could make this question more relevant to the chemistry site by asking about the intermolecular interactions during synthesis that make mis-incorporation highly unlikely, even though in double-helical RNA segments, there is a large variety of pairings including purine:purine or pyrimidine:pyrimidine (so they "fit" into a double helix just fine). $\endgroup$ – Karsten Theis Feb 3 at 21:39

Can't there ever be hydrogen bonds between 2 purines or between 2 pyrimidines?

Yes, it is possible to have hydrogen-bonded base pairs (and triplets and quadruplexes) beyond the canonical Watson-Crick base pairs A:T and G:C. You can explore these in 3D on the DSSR-Jmol site for example. If you look at the 1ehz structure (a tRNA from yeast), which loads automatically on DSSR-Jmol, and click on non-canonical base pairs, you will see some examples. Below is an A:A pair with two symmetric hydrogen bonds from that structure:

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