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Molecular structure differences between Uracil and thymine

Aug 20，2024

Uracil (U) and thymine (T) are both nitrogenous bases in the genetic information of genes and play an important role in the structure and function of nucleic acids (DNA and RNA). Uracil is found in RNA, bound to adenine through two hydrogen bonds, and in DNA, the uracil nucleobase is replaced by thymine. Uracil is the demethylated form of thymine (Figure 1).

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(1) Stability: The presence of methyl groups in thymine makes it more resistant to oxidative damage and hydrolytic cleavage than uracil. This makes DNA more chemically stable than RNA.

(2) Mutability: Cytosine can spontaneously deaminate to form uracil. This has little effect in RNA and only affects the function of specific RNA molecules, and the incidence is small. However, mispairing during DNA replication will lead to persistent and unavoidable genetic errors, which can easily lead to mutational diseases.

(3) Methylated structure: The methyl group in thymine can be enzymatically modified to regulate gene expression through epigenetic mechanisms such as DNA methylation. In contrast, uracil lacks this methylation-based regulatory potential. Methylation also prevents nuclease and incorrect replacement of thymine with cytosine.

In a study of the solvation structure and hydrogen bonding kinetics of uracil-water and thymine-water it was also shown that thymine has higher hydrogen bonding interactions with water molecules than uracil. The dipole rotation of thymine in water was significantly slower than that of uracil. The water-water hydrogen bond is longer-lived compared to the uracil/thymine-water hydrogen bond. The Karplus and Kollman models for thymine showed higher solvation free energy (SFE). At 298 K, the solvation free energy of uracil in the Karplus and Kollman models is closer to the experimentally reported value (-16.06 kcal/mol).

References:

[1] CHINMAY PARIDA; Snehasis C. Solvation structure and hydrogen bond dynamics of uracil–water and thymine–water: A comparison of different force fields of uracil and thymine[J]. Chemical Physics Letters, 2024. DOI:10.1016/j.cplett.2024.141357.

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