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why does dna contain thymine instead of uracil

In DNA molecules, the occurrence of thymine is associated with the occurrence of desoxy-D-ribose. In RNA, the occurrence of uracil is associated with the occurrence of D-ribose. In addition, it is known that the DNA strands form dimers and the RNA strands, oppositely, form no dimers. I think that these differences between DNA and RNA are explained by one cause. This cause may be of structural or thermodynamic nature. I think that this cause is of structural nature, and we intend to study this assumption on the basis of the techniques described in the work: E. A. Kadyshevich, A. V. Dzyabchenko, and V. E. Ostrovskii, Life Origination Hydrate hypothesis (LOH-hypothesis): computer simulation of rearrangement of different DNA components within CH4-hydrate structure II, EPSC Abstracts Vol. 8, EPSC2013-285, 2013 (is available at the ResearchGate as well as other our works about the Hydrate Hypothesis of Living Matter Origintion (LOH-hypothesis) and Mitosis and Replication Hydrate Hypothesis (MRH-hypothesis)).

Apparently, the occurrence of one of these peculiarities determines the two other ones as the geometric consequence. We showed that DNAs (and RNAs) originated within the methane-hydrate matrix and that water structuring-destructuring determines the DNA replication process. In addition, we showed that the thymine-adenine distance within the methane-hydrate structure II is equal to the thymine-adenine distance determined by X-ray techniques in the crystalline DNA double helixes; this result allows the conclusion that DNA double helixes form at the step of DNA formation within the gas-hydrate matrix. We believe that further studies of the DNA/hydrate-matrix systems will allow clarification of the question under consideration.
Thymine has a greater resistance to photochemical mutation, making the genetic message more stable. This offers a rough explanation of why thymine is more protected then uracil.

However, the real question is: Why does thymine replace uracil in DNA? The important thing to notice is that while uracil exists as both uridine (U) and deoxy-uridine (dU), thymine only exists as deoxy-thymidine (dT). So the question becomes: Why do cells go to the trouble of methylating uracil to thymine before it can be used in DNA? and the easy answer is: methylation protects the DNA. Besides using dT instead of dU, most organisms also use various enzymes to modify DNA after it has been synthesized. Two such enzymes, methylate adenines and cytosines, respectively, along the entire DNA strand. This methylation makes the DNA unrecognizable to many nucleases (enzymes which break down DNA and RNA), so that it cannot be easily attacked by invaders, like viruses or certain bacteria. Obviously, methylating the nucleotides before they are incorporated ensures that the entire strand of DNA is protected.

Thymine also protects the DNA in another way. If you look at the components of nucleic acids, phosphates, sugars, and bases, you see that they are all very hydrophilic (water soluble). Obviously, adding a hydrophobic (water insoluble) methyl group to part of the DNA is going to change the characteristics of the molecule. The major effect is that the methyl group will be repelled by the rest of the DNA, moving it to a fixed position in the major groove of the helix. This solves an important problem with uracil - though it prefers adenine, uracil can base-pair with almost any other base, including itself, depending on how it situates itself in the helix. By tacking it down to a single conformation, the methyl group restricts uracil (thymine) to pairing only with adenine. This greatly improves the efficiency of DNA replication, by reducing the rate of mismatches, and thus mutations.

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