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Cytosine should not ever pair with thymine, for two major reasons:

Cytosine and thymine are both pyrimidines, meaning they contain a single sugar, whereas adenine and guanine are purine and contain a two-ringed sugar. If cytosine were to pair with thymine (or another cytosine) it would throw off the shape of the DNA double helix.

Cytosine wants to form three hydrogen bonds, and thymine can only form two.

Thus, under normal circumstances, cytosine will never be paired with thymine.

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