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Well I was wondering why adenine pairs with thymine and cytosine pairs with guanine.

From those pictures:

enter image description here

enter image description here

Thymine has the lowest acidity and adenine has the biggest acidity.

So it is logical that the intermolecular bond will be strong.

Adenine and Cytosine have pretty much the same acidity so why is it energetically favorable for guanine to make an intermolecular bond with cytosine?

Is it due to the three combinations this (adenine-thymine, cytosine, guanine) has the lowest energy?

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closed as unclear what you're asking by Mithoron, Mathew Mahindaratne, Buck Thorn, A.K., Todd Minehardt Sep 5 at 23:13

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    $\begingroup$ Simplest explanation in that only in G-C there can be 3 hydrogen bonds - 3 beats 2. BTW your reasoning is based on false assumptions as there's no such correlation. $\endgroup$ – Mithoron Sep 3 at 21:11
  • $\begingroup$ Thymine is the least acidic since it contains 2 O bases. $\endgroup$ – user82418 Sep 3 at 22:13
  • $\begingroup$ Adenine doesnt contain any 0 bases so it is the most acidic. $\endgroup$ – user82418 Sep 3 at 22:13
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    $\begingroup$ I looked, but I disagree. If you want to have someone look at your comment, use their username prefixed by @, as in @Software_Player. $\endgroup$ – Karsten Theis Sep 3 at 22:17
  • $\begingroup$ @Karsten Theis Why do you disagree? O base is less acidic than N base... $\endgroup$ – user82418 Sep 3 at 22:18
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In Principles of Nucleic Acid Structure, W. Saenger argues that hydrogen-bonded bases contain at least two hydrogen bonds (forming a "cyclic" pattern). Often, there is a tautomeric form possible that also makes two hydrogen bonds, with two covalent bonds turning into hydrogen bonds, two hydrogen bonds turning into covalent bonds, and double bonds moving around so that each atom still has an octet. In the OPs first example (A:T pair), for example, the ketone would turn into an enol, and the protonation of the amino and imino groups would change.

Saenger goes on to say that 28 pairs are possible.

enter image description here

Many of these are observed (the ones that are labeled are so common that they were given names), in structures of DNA, RNA, and in crystal structures of dinucleotides.

I was wondering why adenine pairs with thymine and cytosine pairs with guanine.

They pair because they make strong hydrogen bonds with a geometry of the base pairs that allows base stacking and is compatible with base pairing of the other nucleotides in a DNA strand. As the discussion above shows, many other base pairs are theoretically possible, and some of them are actually observed in nature.

Thymine has the lowest acidity and adenine has the biggest acidity. So it is logical that the intermolecular bond will be strong.

I'm not sure about the premise, and the conclusion is incorrect, as other base pairs also form. As long as a group has the right protonation state, the pKa does not directly determine hydrogen bond strength.

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  • $\begingroup$ Hydrogen bond strength (any intermolecular bond strength) is determined by the polarity of the molecules. $\endgroup$ – user82418 Sep 3 at 22:26
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    $\begingroup$ @SoftwarePlayer OK, but is acidity directly correlated with polarity? $\endgroup$ – Karsten Theis Sep 3 at 22:27
  • $\begingroup$ In Hydrogen bonding , Hydrogen is charged partially positive , so this makes the molecule acidic.By definition an acid is a molecule which can donate a proton so yes. $\endgroup$ – user82418 Sep 3 at 22:30