If you were to try and pair a thymine with a cytosine (a non Watson-Crick base pairing), then would you expect to see any stability with respect to the hydrogen bonding (assuming the geometrical configurations of both bases were favorable to each other)? If yes, then how many hydrogen bonds could form between these two bases?

Yes, two hydrogen bonds could form between thymine and cytosine.

Explanation:

Cytosine is a pyrimidine base found in both DNA and RNA, and Thymine is a pyrimidine base found in only DNA. Electronegative Oxygen and Nitrogen atoms with free lone pairs are potential hydrogen bond acceptors. Hydrogen atoms attached to very electronegative atoms like Oxygen and Nitrogen have strong partial positive charge and are potential hydrogen bond donors.

One hydrogen bond could form between the C4 carbonyl group on thymine which is a hydrogen bond acceptor and the C4 amino group on cytosine which is a hydrogen bond donor. Also, another hydrogen bond could be formed between N3 of thymine which is a hydrogen bond donor and the N3 of cytosine that is a hydrogen bond acceptor.

It is important to note that hydrogen bond cannot be formed between them because the C2 carbonyl groups found on both bases are both hydrogen bond acceptors.

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